Thesis/thesis.lyx

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\begin_body

\begin_layout Title
Bioinformatic analysis of complex, high-throughput genomic and epigenomic
 data in the context of immunology and transplant rejection
\end_layout

\begin_layout Author
A thesis presented 
\begin_inset Newline newline
\end_inset

by
\begin_inset Newline newline
\end_inset

 Ryan C.
 Thompson
\begin_inset Newline newline
\end_inset

 to
\begin_inset Newline newline
\end_inset

 The Scripps Research Institute Graduate Program 
\begin_inset Newline newline
\end_inset

in partial fulfillment of the requirements for the degree of
\begin_inset Newline newline
\end_inset

 Doctor of Philosophy in the subject of Biology
\begin_inset Newline newline
\end_inset

 for
\begin_inset Newline newline
\end_inset

 The Scripps Research Institute
\begin_inset Newline newline
\end_inset

 La Jolla, California
\end_layout

\begin_layout Date
May 2019
\end_layout

\begin_layout Standard
[Copyright notice]
\end_layout

\begin_layout Standard
[Thesis acceptance form]
\end_layout

\begin_layout Standard
[Dedication]
\end_layout

\begin_layout Standard
[Acknowledgements]
\end_layout

\begin_layout Standard
\begin_inset CommandInset toc
LatexCommand tableofcontents

\end_inset


\end_layout

\begin_layout Standard
\begin_inset FloatList table

\end_inset


\end_layout

\begin_layout Standard
\begin_inset FloatList figure

\end_inset


\end_layout

\begin_layout Standard
[List of Abbreviations] 
\begin_inset Note Note
status open

\begin_layout Plain Layout
https://wiki.lyx.org/Tips/Nomenclature
\end_layout

\end_inset


\end_layout

\begin_layout Standard
[Abstract]
\end_layout

\begin_layout Chapter*
Abstract
\end_layout

\begin_layout Chapter
Introduction
\end_layout

\begin_layout Section
Background & Significance
\end_layout

\begin_layout Subsection
Biological motivation
\end_layout

\begin_layout Itemize
Rejection is the major long-term threat to organ and tissue grafts
\end_layout

\begin_deeper
\begin_layout Itemize
Common mechanisms of rejection 
\end_layout

\begin_layout Itemize
Effective immune suppression requires monitoring for rejection and tuning
 
\end_layout

\begin_layout Itemize
Current tests for rejection (tissue biopsy) are invasive and biased 
\end_layout

\begin_layout Itemize
A blood test based on microarrays would be less biased and invasive
\end_layout

\end_deeper
\begin_layout Itemize
Memory cells are resistant to immune suppression
\end_layout

\begin_deeper
\begin_layout Itemize
Mechanisms of resistance in memory cells are poorly understood 
\end_layout

\begin_layout Itemize
A better understanding of immune memory formation is needed
\end_layout

\end_deeper
\begin_layout Itemize
Mesenchymal stem cell infusion is a promising new treatment to prevent/delay
 rejection
\end_layout

\begin_deeper
\begin_layout Itemize
Demonstrated in mice, but not yet in primates
\end_layout

\begin_layout Itemize
Mechanism currently unknown, but MSC are known to be immune modulatory
\end_layout

\end_deeper
\begin_layout Subsection
Overview of bioinformatic analysis methods
\end_layout

\begin_layout Standard
An overview of all the methods used, including what problem they solve,
 what assumptions they make, and a basic description of how they work.
\end_layout

\begin_layout Itemize
ChIP-seq Peak calling
\end_layout

\begin_deeper
\begin_layout Itemize
Cross-correlation analysis to determine fragment size
\end_layout

\begin_layout Itemize
Broad vs narrow peaks
\end_layout

\begin_layout Itemize
SICER for broad peaks
\end_layout

\begin_layout Itemize
IDR for biologically reproducible peaks
\end_layout

\begin_layout Itemize
csaw peak filtering guidelines for unbiased downstream analysis
\end_layout

\end_deeper
\begin_layout Itemize
Normalization is non-trivial and application-dependant
\end_layout

\begin_deeper
\begin_layout Itemize
Expression arrays: RMA & fRMA; why fRMA is needed
\end_layout

\begin_layout Itemize
Methylation arrays: M-value transformation approximates normal data but
 induces heteroskedasticity
\end_layout

\begin_layout Itemize
RNA-seq: normalize based on assumption that the average gene is not changing
\end_layout

\begin_layout Itemize
ChIP-seq: complex with many considerations, dependent on experimental methods,
 biological system, and analysis goals
\end_layout

\end_deeper
\begin_layout Itemize
Limma: The standard linear modeling framework for genomics
\end_layout

\begin_deeper
\begin_layout Itemize
empirical Bayes variance modeling: limma's core feature
\end_layout

\begin_layout Itemize
edgeR & DESeq2: Extend with negative bonomial GLM for RNA-seq and other
 count data
\end_layout

\begin_layout Itemize
voom: Extend with precision weights to model mean-variance trend
\end_layout

\begin_layout Itemize
arrayWeights and duplicateCorrelation to handle complex variance structures
\end_layout

\end_deeper
\begin_layout Itemize
sva and ComBat for batch correction
\end_layout

\begin_layout Itemize
Factor analysis: PCA, MDS, MOFA
\end_layout

\begin_deeper
\begin_layout Itemize
Batch-corrected PCA is informative, but careful application is required
 to avoid bias
\end_layout

\end_deeper
\begin_layout Itemize
Gene set analysis: camera and SPIA
\end_layout

\begin_layout Section
Innovation
\end_layout

\begin_layout Itemize
MSC infusion to improve transplant outcomes (prevent/delay rejection)
\end_layout

\begin_deeper
\begin_layout Itemize
Characterize MSC response to interferon gamma
\end_layout

\begin_layout Itemize
IFN-g is thought to stimulate their function
\end_layout

\begin_layout Itemize
Test IFN-g treated MSC infusion as a therapy to delay graft rejection in
 cynomolgus monkeys
\end_layout

\begin_layout Itemize
Monitor animals post-transplant using blood RNA-seq at serial time points
\end_layout

\end_deeper
\begin_layout Itemize
Investigate dynamics of histone marks in CD4 T-cell activation and memory
\end_layout

\begin_deeper
\begin_layout Itemize
Previous studies have looked at single snapshots of histone marks
\end_layout

\begin_layout Itemize
Instead, look at changes in histone marks across activation and memory
\end_layout

\end_deeper
\begin_layout Itemize
High-throughput sequencing and microarray technologies
\end_layout

\begin_deeper
\begin_layout Itemize
Powerful methods for assaying gene expression and epigenetics across entire
 genomes
\end_layout

\begin_layout Itemize
Proper analysis requires finding and exploiting systematic genome-wide trends
\end_layout

\end_deeper
\begin_layout Chapter
Reproducible genome-wide epigenetic analysis of H3K4 and H3K27 methylation
 in naive and memory CD4 T-cell activation
\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
Author list: Me, Sarah, Dan
\end_layout

\end_inset


\end_layout

\begin_layout Section
Approach
\end_layout

\begin_layout Itemize
CD4 T-cells are central to all adaptive immune responses and memory
\end_layout

\begin_layout Itemize
H3K4 and H3K27 methylation are major epigenetic regulators of gene expression
\end_layout

\begin_layout Itemize
Canonically, H3K4 is activating and H3K27 is inhibitory, but the reality
 is complex
\end_layout

\begin_layout Itemize
Looking at these marks during CD4 activation and memory should reveal new
 mechanistic details
\end_layout

\begin_layout Itemize
Test 
\begin_inset Quotes eld
\end_inset

poised promoter
\begin_inset Quotes erd
\end_inset

 hypothesis in which H3K4 and H3K27 are both methylated
\end_layout

\begin_layout Itemize
Expand scope of analysis beyond simple promoter counts
\end_layout

\begin_deeper
\begin_layout Itemize
Analyze peaks genome-wide, including in intergenic regions
\end_layout

\begin_layout Itemize
Analysis of coverage distribution shape within promoters, e.g.
 upstream vs downstream coverage
\end_layout

\end_deeper
\begin_layout Section
Methods
\end_layout

\begin_layout Itemize
Re-analyze previously published CD4 ChIP-seq & RNA-seq data 
\begin_inset CommandInset citation
LatexCommand cite
key "LaMere2016,Lamere2017"
literal "true"

\end_inset


\end_layout

\begin_deeper
\begin_layout Itemize
Completely reimplement analysis from scratch as a reproducible workflow
\end_layout

\begin_layout Itemize
Use newly published methods & algorithms not available during the original
 analysis: SICER, csaw, MOFA, ComBat, sva, GREAT, and more
\end_layout

\end_deeper
\begin_layout Itemize
SICER, IDR, csaw, & GREAT to call ChIP-seq peaks genome-wide, perform differenti
al abundance analysis, and relate those peaks to gene expression
\end_layout

\begin_layout Itemize
Promoter counts in sliding windows around each gene's highest-expressed
 TSS to investigate coverage distribution within promoters
\end_layout

\begin_layout Section
Results
\end_layout

\begin_layout Itemize
Different histone marks have different effective promoter radii
\end_layout

\begin_layout Itemize
H3K4 and RNA-seq data show clear evidence of naive convergence with memory
 between days 1 and 5
\end_layout

\begin_layout Itemize
Promoter coverage distribution affects gene expression independent of total
 promoter count
\end_layout

\begin_layout Itemize
Remaining analyses to complete:
\end_layout

\begin_deeper
\begin_layout Itemize
Look for naive-to-memory convergence in H3K27 data
\end_layout

\begin_layout Itemize
Look at enriched pathways for day 0 to day 1 (activation) compared to day
 1 to day 5 (putative naive-to-memory differentiation)
\end_layout

\begin_layout Itemize
Find genes with different expression patterns in naive vs.
 memory and try to explain the difference with the Day 0 histone mark data
\end_layout

\begin_deeper
\begin_layout Itemize
Determine whether co-occurrence of H3K4me3 and H3K27me3 (proposed 
\begin_inset Quotes eld
\end_inset

poised
\begin_inset Quotes erd
\end_inset

 state) has effects on post-activation expression dynamics
\end_layout

\begin_layout Itemize
Promoter coverage distribution dynamics throughout activation for interesting
 subsets of genes
\end_layout

\end_deeper
\begin_layout Itemize
(Backup) Compare and contrast behavior of promoter peaks vs intergenic (putative
 enhancer) peaks (GREAT analysis)
\end_layout

\begin_deeper
\begin_layout Itemize
Put results in context of important T-cell pathways & gene expression data
\end_layout

\end_deeper
\end_deeper
\begin_layout Section
Discussion
\end_layout

\begin_layout Itemize
"Promoter radius" is not constant and must be defined empirically for a
 given data set
\end_layout

\begin_layout Itemize
Evaluate evidence for poised promoters and enhancer effects on gene expression
 dynamics of naive-to-memory differentiation
\end_layout

\begin_layout Itemize
Compare to published work on other epigenetic marks (e.g.
 chromatin accessibility)
\end_layout

\begin_layout Chapter
Improving array-based analyses of transplant rejection by optimizing data
 preprocessing
\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
Author list: Me, Sunil, Padma, Dan
\end_layout

\end_inset


\end_layout

\begin_layout Section
Approach
\end_layout

\begin_layout Itemize
Machine-learning applications demand a "single-channel" normalization method
\end_layout

\begin_layout Itemize
frozen RMA is a good solution, but not trivial to apply
\end_layout

\begin_layout Itemize
Methylation array data preprocessing induces heteroskedasticity
\end_layout

\begin_layout Itemize
Need to account for this mean-variance dependency in analysis
\end_layout

\begin_layout Section
Methods
\end_layout

\begin_layout Itemize
Expression array normalization for detecting acute rejection
\end_layout

\begin_layout Itemize
Use frozen RMA, a single-channel variant of RMA
\end_layout

\begin_layout Itemize
Generate custom fRMA normalization vectors for each tissue (biopsy, blood)
\end_layout

\begin_layout Itemize
Methylation arrays for differential methylation in rejection vs.
 healthy transplant
\end_layout

\begin_layout Itemize
Adapt voom method originally designed for RNA-seq to model mean-variance
 dependence
\end_layout

\begin_layout Itemize
Use sample precision weighting and sva to adjust for other confounding factors
\end_layout

\begin_layout Section
Results
\end_layout

\begin_layout Itemize
custom fRMA normalization improved cross-validated classifier performance
 
\begin_inset CommandInset citation
LatexCommand cite
key "Kurian2014"
literal "true"

\end_inset


\end_layout

\begin_layout Itemize
voom, precision weights, and sva improved model fit
\end_layout

\begin_deeper
\begin_layout Itemize
Also increased sensitivity for detecting differential methylation
\end_layout

\end_deeper
\begin_layout Section
Discussion
\end_layout

\begin_layout Itemize
fRMA enables classifying new samples without re-normalizing the entire data
 set
\end_layout

\begin_deeper
\begin_layout Itemize
Critical for translating a classifier into clinical practice
\end_layout

\end_deeper
\begin_layout Itemize
Methods like voom designed for RNA-seq can also help with array analysis
\end_layout

\begin_layout Itemize
Extracting and modeling confounders common to many features improves model
 correspondence to known biology
\end_layout

\begin_layout Chapter
Globin-blocking for more effective blood RNA-seq analysis in primate animal
 model
\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
TODO Choose between above and the paper title: Optimizing yield of deep
 RNA sequencing for gene expression profiling by globin reduction of peripheral
 blood samples from cynomolgus monkeys (Macaca fascicularis).
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
How to integrate/credit sections written by others (e.g.
 wetlab methods)? (Majority of paper text is written by me.)Preprint the
 paper, then cite it.
 Every chapter has an author list, which may or may not be part of a citation
 to a published/preprinted paper.
\end_layout

\begin_layout Plain Layout
TODO: Preprint the paper, then cite it.
\end_layout

\begin_layout Plain Layout
TODO: Chapter author list: https://tex.stackexchange.com/questions/156862/displayi
ng-author-for-each-chapter-in-book
\end_layout

\end_inset


\end_layout

\begin_layout Section*
Abstract
\end_layout

\begin_layout Paragraph
Background
\end_layout

\begin_layout Standard
Primate blood contains high concentrations of globin messenger RNA.
 Globin reduction is a standard technique used to improve the expression
 results obtained by DNA microarrays on RNA from blood samples.
 However, with whole transcriptome RNA-sequencing (RNA-seq) quickly replacing
 microarrays for many applications, the impact of globin reduction for RNA-seq
 has not been previously studied.
 Moreover, no off-the-shelf kits are available for globin reduction in nonhuman
 primates.
 
\end_layout

\begin_layout Paragraph
Results
\end_layout

\begin_layout Standard
Here we report a protocol for RNA-seq in primate blood samples that uses
 complimentary oligonucleotides to block reverse transcription of the alpha
 and beta globin genes.
 In test samples from cynomolgus monkeys (Macaca fascicularis), this globin
 blocking protocol approximately doubles the yield of informative (non-globin)
 reads by greatly reducing the fraction of globin reads, while also improving
 the consistency in sequencing depth between samples.
 The increased yield enables detection of about 2000 more genes, significantly
 increases the correlation in measured gene expression levels between samples,
 and increases the sensitivity of differential gene expression tests.
\end_layout

\begin_layout Paragraph
Conclusions
\end_layout

\begin_layout Standard
These results show that globin blocking significantly improves the cost-effectiv
eness of mRNA sequencing in primate blood samples by doubling the yield
 of useful reads, allowing detection of more genes, and improving the precision
 of gene expression measurements.
 Based on these results, a globin reducing or blocking protocol is recommended
 for all RNA-seq studies of primate blood samples.
\end_layout

\begin_layout Section
Approach
\end_layout

\begin_layout Itemize
Cynomolgus monkeys as a model organism
\end_layout

\begin_deeper
\begin_layout Itemize
Highly related to humans
\end_layout

\begin_layout Itemize
Small size and short life cycle - good research animal
\end_layout

\begin_layout Itemize
Genomics resources still in development
\end_layout

\end_deeper
\begin_layout Itemize
Inadequacy of existing blood RNA-seq protocols
\end_layout

\begin_deeper
\begin_layout Itemize
Existing protocols use a separate globin pulldown step, slowing down processing
\end_layout

\end_deeper
\begin_layout Standard
Increasingly, researchers are turning to high-throughput mRNA sequencing
 technologies (RNA-seq) in preference to expression microarrays for analysis
 of gene expression 
\begin_inset CommandInset citation
LatexCommand cite
key "Mutz2012"
literal "false"

\end_inset

.
 The advantages are even greater for study of model organisms with no well-estab
lished array platforms available, such as the cynomolgus monkey (Macaca
 fascicularis).
 High fractions of globin mRNA are naturally present in mammalian peripheral
 blood samples (up to 70% of total mRNA) and these are known to interfere
 with the results of array-based expression profiling 
\begin_inset CommandInset citation
LatexCommand cite
key "Winn2010"
literal "false"

\end_inset

.
 The importance of globin reduction for RNA-seq of blood has only been evaluated
 for a deepSAGE protocol on human samples 
\begin_inset CommandInset citation
LatexCommand cite
key "Mastrokolias2012"
literal "false"

\end_inset

.
 In the present report, we evaluated globin reduction using custom blocking
 oligonucleotides for deep RNA-seq of peripheral blood samples from a nonhuman
 primate, cynomolgus monkey, using the Illumina technology platform.
 We demonstrate that globin reduction significantly improves the cost-effectiven
ess of RNA-seq in blood samples.
 Thus, our protocol offers a significant advantage to any investigator planning
 to use RNA-seq for gene expression profiling of nonhuman primate blood
 samples.
 Our method can be generally applied to any species by designing complementary
 oligonucleotide blocking probes to the globin gene sequences of that species.
 Indeed, any highly expressed but biologically uninformative transcripts
 can also be blocked to further increase sequencing efficiency and value
 
\begin_inset CommandInset citation
LatexCommand cite
key "Arnaud2016"
literal "false"

\end_inset

.
\end_layout

\begin_layout Section
Methods
\end_layout

\begin_layout Subsection*
Sample collection
\end_layout

\begin_layout Standard
All research reported here was done under IACUC-approved protocols at the
 University of Miami and complied with all applicable federal and state
 regulations and ethical principles for nonhuman primate research.
 Blood draws occurred between 16 April 2012 and 18 June 2015.
 The experimental system involved intrahepatic pancreatic islet transplantation
 into Cynomolgus monkeys with induced diabetes mellitus with or without
 concomitant infusion of mesenchymal stem cells.
 Blood was collected at serial time points before and after transplantation
 into PAXgene Blood RNA tubes (PreAnalytiX/Qiagen, Valencia, CA) at the
 precise volume:volume ratio of 2.5 ml whole blood into 6.9 ml of PAX gene
 additive.
\end_layout

\begin_layout Subsection*
Globin Blocking
\end_layout

\begin_layout Standard
Four oligonucleotides were designed to hybridize to the 3’ end of the transcript
s for Cynomolgus HBA1, HBA2 and HBB, with two hybridization sites for HBB
 and 2 sites for HBA (the chosen sites were identical in both HBA genes).
 All oligos were purchased from Sigma and were entirely composed of 2’O-Me
 bases with a C3 spacer positioned at the 3’ ends to prevent any polymerase
 mediated primer extension.
\end_layout

\begin_layout Quote
HBA1/2 site 1: GCCCACUCAGACUUUAUUCAAAG-C3spacer
\end_layout

\begin_layout Quote
HBA1/2 site 2: GGUGCAAGGAGGGGAGGAG-C3spacer
\end_layout

\begin_layout Quote
HBB site 1: AAUGAAAAUAAAUGUUUUUUAUUAG-C3spacer
\end_layout

\begin_layout Quote
HBB site 2: CUCAAGGCCCUUCAUAAUAUCCC-C3spacer
\end_layout

\begin_layout Subsection*
RNA-seq Library Preparation 
\end_layout

\begin_layout Standard
Sequencing libraries were prepared with 200ng total RNA from each sample.
 Polyadenylated mRNA was selected from 200 ng aliquots of cynomologus blood-deri
ved total RNA using Ambion Dynabeads Oligo(dT)25 beads (Invitrogen) following
 manufacturer’s recommended protocol.
 PolyA selected RNA was then combined with 8 pmol of HBA1/2 (site 1), 8
 pmol of HBA1/2 (site 2), 12 pmol of HBB (site 1) and 12 pmol of HBB (site
 2) oligonucleotides.
 In addition, 20 pmol of RT primer containing a portion of the Illumina
 adapter sequence (B-oligo-dTV: GAGTTCCTTGGCACCCGAGAATTCCATTTTTTTTTTTTTTTTTTTV)
 and 4 µL of 5X First Strand buffer (250 mM Tris-HCl pH 8.3, 375 mM KCl,
 15mM MgCl2) were added in a total volume of 15 µL.
 The RNA was fragmented by heating this cocktail for 3 minutes at 95°C and
 then placed on ice.
 This was followed by the addition of 2 µL 0.1 M DTT, 1 µL RNaseOUT, 1 µL
 10mM dNTPs 10% biotin-16 aminoallyl-2’- dUTP and 10% biotin-16 aminoallyl-2’-
 dCTP (TriLink Biotech, San Diego, CA), 1 µL Superscript II (200U/ µL, Thermo-Fi
sher).
 A second “unblocked” library was prepared in the same way for each sample
 but replacing the blocking oligos with an equivalent volume of water.
 The reaction was carried out at 25°C for 15 minutes and 42°C for 40 minutes,
 followed by incubation at 75°C for 10 minutes to inactivate the reverse
 transcriptase.
\end_layout

\begin_layout Standard
The cDNA/RNA hybrid molecules were purified using 1.8X Ampure XP beads (Agencourt
) following supplier’s recommended protocol.
 The cDNA/RNA hybrid was eluted in 25 µL of 10 mM Tris-HCl pH 8.0, and then
 bound to 25 µL of M280 Magnetic Streptavidin beads washed per recommended
 protocol (Thermo-Fisher).
 After 30 minutes of binding, beads were washed one time in 100 µL 0.1N NaOH
 to denature and remove the bound RNA, followed by two 100 µL washes with
 1X TE buffer.
\end_layout

\begin_layout Standard
Subsequent attachment of the 5-prime Illumina A adapter was performed by
 on-bead random primer extension of the following sequence (A-N8 primer:
 TTCAGAGTTCTACAGTCCGACGATCNNNNNNNN).
 Briefly, beads were resuspended in a 20 µL reaction containing 5 µM A-N8
 primer, 40mM Tris-HCl pH 7.5, 20mM MgCl2, 50mM NaCl, 0.325U/µL Sequenase
 2.0 (Affymetrix, Santa Clara, CA), 0.0025U/µL inorganic pyrophosphatase (Affymetr
ix) and 300 µM each dNTP.
 Reaction was incubated at 22°C for 30 minutes, then beads were washed 2
 times with 1X TE buffer (200µL).
\end_layout

\begin_layout Standard
The magnetic streptavidin beads were resuspended in 34 µL nuclease-free
 water and added directly to a PCR tube.
 The two Illumina protocol-specified PCR primers were added at 0.53 µM (Illumina
 TruSeq Universal Primer 1 and Illumina TruSeq barcoded PCR primer 2), along
 with 40 µL 2X KAPA HiFi Hotstart ReadyMix (KAPA, Willmington MA) and thermocycl
ed as follows: starting with 98°C (2 min-hold); 15 cycles of 98°C, 20sec;
 60°C, 30sec; 72°C, 30sec; and finished with a 72°C (2 min-hold).
\end_layout

\begin_layout Standard
PCR products were purified with 1X Ampure Beads following manufacturer’s
 recommended protocol.
 Libraries were then analyzed using the Agilent TapeStation and quantitation
 of desired size range was performed by “smear analysis”.
 Samples were pooled in equimolar batches of 16 samples.
 Pooled libraries were size selected on 2% agarose gels (E-Gel EX Agarose
 Gels; Thermo-Fisher).
 Products were cut between 250 and 350 bp (corresponding to insert sizes
 of 130 to 230 bps).
 Finished library pools were then sequenced on the Illumina NextSeq500 instrumen
t with 75 base read lengths.
 
\end_layout

\begin_layout Subsection*
Read alignment and counting
\end_layout

\begin_layout Standard
Reads were aligned to the cynomolgus genome using STAR 
\begin_inset CommandInset citation
LatexCommand cite
key "Dobin2013,Wilson2013"
literal "false"

\end_inset

.
 Counts of uniquely mapped reads were obtained for every gene in each sample
 with the “featureCounts” function from the Rsubread package, using each
 of the three possibilities for the “strandSpecific” option: sense, antisense,
 and unstranded 
\begin_inset CommandInset citation
LatexCommand cite
key "Liao2014"
literal "false"

\end_inset

.
 A few artifacts in the cynomolgus genome annotation complicated read counting.
 First, no ortholog is annotated for alpha globin in the cynomolgus genome,
 presumably because the human genome has two alpha globin genes with nearly
 identical sequences, making the orthology relationship ambiguous.
 However, two loci in the cynomolgus genome are as “hemoglobin subunit alpha-lik
e” (LOC102136192 and LOC102136846).
 LOC102136192 is annotated as a pseudogene while LOC102136846 is annotated
 as protein-coding.
 Our globin reduction protocol was designed to include blocking of these
 two genes.
 Indeed, these two genes have almost the same read counts in each library
 as the properly-annotated HBB gene and much larger counts than any other
 gene in the unblocked libraries, giving confidence that reads derived from
 the real alpha globin are mapping to both genes.
 Thus, reads from both of these loci were counted as alpha globin reads
 in all further analyses.
 The second artifact is a small, uncharacterized non-coding RNA gene (LOC1021365
91), which overlaps the HBA-like gene (LOC102136192) on the opposite strand.
 If counting is not performed in stranded mode (or if a non-strand-specific
 sequencing protocol is used), many reads mapping to the globin gene will
 be discarded as ambiguous due to their overlap with this ncRNA gene, resulting
 in significant undercounting of globin reads.
 Therefore, stranded sense counts were used for all further analysis in
 the present study to insure that we accurately accounted for globin transcript
 reduction.
 However, we note that stranded reads are not necessary for RNA-seq using
 our protocol in standard practice.
 
\end_layout

\begin_layout Subsection*
Normalization and Exploratory Data Analysis
\end_layout

\begin_layout Standard
Libraries were normalized by computing scaling factors using the edgeR package’s
 Trimmed Mean of M-values method 
\begin_inset CommandInset citation
LatexCommand cite
key "Robinson2010"
literal "false"

\end_inset

.
 Log2 counts per million values (logCPM) were calculated using the cpm function
 in edgeR for individual samples and aveLogCPM function for averages across
 groups of samples, using those functions’ default prior count values to
 avoid taking the logarithm of 0.
 Genes were considered “present” if their average normalized logCPM values
 across all libraries were at least -1.
 Normalizing for gene length was unnecessary because the sequencing protocol
 is 3’-biased and hence the expected read count for each gene is related
 to the transcript’s copy number but not its length.
\end_layout

\begin_layout Standard
In order to assess the effect of blocking on reproducibility, Pearson and
 Spearman correlation coefficients were computed between the logCPM values
 for every pair of libraries within the globin-blocked (GB) and unblocked
 (non-GB) groups, and edgeR's “estimateDisp” function was used to compute
 negative binomial dispersions separately for the two groups 
\begin_inset CommandInset citation
LatexCommand cite
key "Chen2014"
literal "false"

\end_inset

.
\end_layout

\begin_layout Subsection*
Differential Expression Analysis
\end_layout

\begin_layout Standard
All tests for differential gene expression were performed using edgeR, by
 first fitting a negative binomial generalized linear model to the counts
 and normalization factors and then performing a quasi-likelihood F-test
 with robust estimation of outlier gene dispersions 
\begin_inset CommandInset citation
LatexCommand cite
key "Lund2012,Phipson2016"
literal "false"

\end_inset

.
 To investigate the effects of globin blocking on each gene, an additive
 model was fit to the full data with coefficients for globin blocking and
 SampleID.
 To test the effect of globin blocking on detection of differentially expressed
 genes, the GB samples and non-GB samples were each analyzed independently
 as follows: for each animal with both a pre-transplant and a post-transplant
 time point in the data set, the pre-transplant sample and the earliest
 post-transplant sample were selected, and all others were excluded, yielding
 a pre-/post-transplant pair of samples for each animal (N=7 animals with
 paired samples).
 These samples were analyzed for pre-transplant vs.
 post-transplant differential gene expression while controlling for inter-animal
 variation using an additive model with coefficients for transplant and
 animal ID.
 In all analyses, p-values were adjusted using the Benjamini-Hochberg procedure
 for FDR correction 
\begin_inset CommandInset citation
LatexCommand cite
key "Benjamini1995"
literal "false"

\end_inset

.
\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Itemize
New blood RNA-seq protocol to block reverse transcription of globin genes
\end_layout

\begin_layout Itemize
Blood RNA-seq time course after transplants with/without MSC infusion
\end_layout

\end_inset


\end_layout

\begin_layout Section
Results
\end_layout

\begin_layout Subsection*
Globin blocking yields a larger and more consistent fraction of useful reads
 
\end_layout

\begin_layout Standard
The objective of the present study was to validate a new protocol for deep
 RNA-seq of whole blood drawn into PaxGene tubes from cynomolgus monkeys
 undergoing islet transplantation, with particular focus on minimizing the
 loss of useful sequencing space to uninformative globin reads.
 The details of the analysis with respect to transplant outcomes and the
 impact of mesenchymal stem cell treatment will be reported in a separate
 manuscript (in preparation).
 To focus on the efficacy of our globin blocking protocol, 37 blood samples,
 16 from pre-transplant and 21 from post-transplant time points, were each
 prepped once with and once without globin blocking oligos, and were then
 sequenced on an Illumina NextSeq500 instrument.
 The number of reads aligning to each gene in the cynomolgus genome was
 counted.
 Table 1 summarizes the distribution of read fractions among the GB and
 non-GB libraries.
 In the libraries with no globin blocking, globin reads made up an average
 of 44.6% of total input reads, while reads assigned to all other genes made
 up an average of 26.3%.
 The remaining reads either aligned to intergenic regions (that include
 long non-coding RNAs) or did not align with any annotated transcripts in
 the current build of the cynomolgus genome.
 In the GB libraries, globin reads made up only 3.48% and reads assigned
 to all other genes increased to 50.4%.
 Thus, globin blocking resulted in a 92.2% reduction in globin reads and
 a 91.6% increase in yield of useful non-globin reads.
 
\end_layout

\begin_layout Standard
This reduction is not quite as efficient as the previous analysis showed
 for human samples by DeepSAGE (<0.4% globin reads after globin reduction)
 
\begin_inset CommandInset citation
LatexCommand cite
key "Mastrokolias2012"
literal "false"

\end_inset

.
 Nonetheless, this degree of globin reduction is sufficient to nearly double
 the yield of useful reads.
 Thus, globin blocking cuts the required sequencing effort (and costs) to
 achieve a target coverage depth by almost 50%.
 Consistent with this near doubling of yield, the average difference in
 un-normalized logCPM across all genes between the GB libraries and non-GB
 libraries is approximately 1 (mean = 1.01, median = 1.08), an overall 2-fold
 increase.
 Un-normalized values are used here because the TMM normalization correctly
 identifies this 2-fold difference as biologically irrelevant and removes
 it.
\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename graphics/Globin Paper/figure1 - globin-fractions.pdf

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
Fraction of genic reads in each sample aligned to non-globin genes, with
 and without globin blocking (GB).
 
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "fig:Fraction-of-genic-reads"

\end_inset

Fraction of genic reads in each sample aligned to non-globin genes, with
 and without globin blocking (GB).

\series default
 All reads in each sequencing library were aligned to the cyno genome, and
 the number of reads uniquely aligning to each gene was counted.
 For each sample, counts were summed separately for all globin genes and
 for the remainder of the genes (non-globin genes), and the fraction of
 genic reads aligned to non-globin genes was computed.
 Each point represents an individual sample.
 Gray + signs indicate the means for globin-blocked libraries and unblocked
 libraries.
 The overall distribution for each group is represented as a notched box
 plots.
 Points are randomly spread vertically to avoid excessive overlapping.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Float table
placement p
wide false
sideways true
status open

\begin_layout Plain Layout
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="4" columns="7">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="1" alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
\xout off
\uuline off
\uwave off
\noun off
\color none
Percent of Total Reads
\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="1" alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
\bar no
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\color none
Percent of Genic Reads
\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout
GB
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
\xout off
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\uwave off
\noun off
\color none
Non-globin Reads
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
Globin Reads
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
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\noun off
\color none
All Genic Reads
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
All Aligned Reads
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
Non-globin Reads
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
\xout off
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\noun off
\color none
Globin Reads
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
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\noun off
\color none
Yes
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\color none
50.4% ± 6.82
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
3.48% ± 2.94
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
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\noun off
\color none
53.9% ± 6.81
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
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\color none
89.7% ± 2.40
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
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\color none
93.5% ± 5.25
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
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\color none
6.49% ± 5.25
\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
No
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
26.3% ± 8.95
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
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44.6% ± 16.6
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
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\color none
70.1% ± 9.38
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
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\emph off
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\color none
90.7% ± 5.16
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

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\color none
38.8% ± 17.1
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
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\emph off
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\color none
61.2% ± 17.1
\end_layout

\end_inset
</cell>
</row>
</lyxtabular>

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
Fractions of reads mapping to genomic features in GB and non-GB samples.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "tab:Fractions-of-reads"

\end_inset

Fractions of reads mapping to genomic features in GB and non-GB samples.
 
\series default
All values are given as mean ± standard deviation.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
Another important aspect is that the standard deviations in Table 
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:Fractions-of-reads"
plural "false"
caps "false"
noprefix "false"

\end_inset

 are uniformly smaller in the GB samples than the non-GB ones, indicating
 much greater consistency of yield.
 This is best seen in the percentage of non-globin reads as a fraction of
 total reads aligned to annotated genes (genic reads).
 For the non-GB samples, this measure ranges from 10.9% to 80.9%, while for
 the GB samples it ranges from 81.9% to 99.9% (Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:Fraction-of-genic-reads"
plural "false"
caps "false"
noprefix "false"

\end_inset

).
 This means that for applications where it is critical that each sample
 achieve a specified minimum coverage in order to provide useful information,
 it would be necessary to budget up to 10 times the sequencing depth per
 sample without globin blocking, even though the average yield improvement
 for globin blocking is only 2-fold, because every sample has a chance of
 being 90% globin and 10% useful reads.
 Hence, the more consistent behavior of GB samples makes planning an experiment
 easier and more efficient because it eliminates the need to over-sequence
 every sample in order to guard against the worst case of a high-globin
 fraction.
\end_layout

\begin_layout Subsection*
Globin blocking lowers the noise floor and allows detection of about 2000
 more genes
\end_layout

\begin_layout Standard
\begin_inset Note Note
status collapsed

\begin_layout Plain Layout
TODO Remove extraneous titles from figures
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename graphics/Globin Paper/figure2 - aveLogCPM-colored.pdf

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
Distributions of average group gene abundances when normalized separately
 or together.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "fig:logcpm-dists"

\end_inset

Distributions of average group gene abundances when normalized separately
 or together.

\series default
 All reads in each sequencing library were aligned to the cyno genome, and
 the number of reads uniquely aligning to each gene was counted.
 Genes with zero counts in all libraries were discarded.
 Libraries were normalized using the TMM method.
 Libraries were split into globin-blocked (GB) and non-GB groups and the
 average abundance for each gene in both groups, measured in log2 counts
 per million reads counted, was computed using the aveLogCPM function.
 The distribution of average gene logCPM values was plotted for both groups
 using a kernel density plot to approximate a continuous distribution.
 The logCPM GB distributions are marked in red, non-GB in blue.
 The black vertical line denotes the chosen detection threshold of -1.
 Top panel: Libraries were split into GB and non-GB groups first and normalized
 separately.
 Bottom panel: Libraries were all normalized together first and then split
 into groups.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
Since globin blocking yields more usable sequencing depth, it should also
 allow detection of more genes at any given threshold.
 When we looked at the distribution of average normalized logCPM values
 across all libraries for genes with at least one read assigned to them,
 we observed the expected bimodal distribution, with a high-abundance "signal"
 peak representing detected genes and a low-abundance "noise" peak representing
 genes whose read count did not rise above the noise floor (Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:logcpm-dists"
plural "false"
caps "false"
noprefix "false"

\end_inset

).
 Consistent with the 2-fold increase in raw counts assigned to non-globin
 genes, the signal peak for GB samples is shifted to the right relative
 to the non-GB signal peak.
 When all the samples are normalized together, this difference is normalized
 out, lining up the signal peaks, and this reveals that, as expected, the
 noise floor for the GB samples is about 2-fold lower.
 This greater separation between signal and noise peaks in the GB samples
 means that low-expression genes should be more easily detected and more
 precisely quantified than in the non-GB samples.
\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename graphics/Globin Paper/figure3 - detection.pdf

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
Gene detections as a function of abundance thresholds in globin-blocked
 (GB) and non-GB samples.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "fig:Gene-detections"

\end_inset

Gene detections as a function of abundance thresholds in globin-blocked
 (GB) and non-GB samples.

\series default
 Average abundance (logCPM, 
\begin_inset Formula $\log_{2}$
\end_inset

 counts per million reads counted) was computed by separate group normalization
 as described in Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:logcpm-dists"
plural "false"
caps "false"
noprefix "false"

\end_inset

 for both the GB and non-GB groups, as well as for all samples considered
 as one large group.
 For each every integer threshold from -2 to 3, the number of genes detected
 at or above that logCPM threshold was plotted for each group.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
Based on these distributions, we selected a detection threshold of -1, which
 is approximately the leftmost edge of the trough between the signal and
 noise peaks.
 This represents the most liberal possible detection threshold that doesn't
 call substantial numbers of noise genes as detected.
 Among the full dataset, 13429 genes were detected at this threshold, and
 22276 were not.
 When considering the GB libraries and non-GB libraries separately and re-comput
ing normalization factors independently within each group, 14535 genes were
 detected in the GB libraries while only 12460 were detected in the non-GB
 libraries.
 Thus, GB allowed the detection of 2000 extra genes that were buried under
 the noise floor without GB.
 This pattern of at least 2000 additional genes detected with GB was also
 consistent across a wide range of possible detection thresholds, from -2
 to 3 (see Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:Gene-detections"
plural "false"
caps "false"
noprefix "false"

\end_inset

).
\end_layout

\begin_layout Subsection*
Globin blocking does not add significant additional noise or decrease sample
 quality
\end_layout

\begin_layout Standard
One potential worry is that the globin blocking protocol could perturb the
 levels of non-globin genes.
 There are two kinds of possible perturbations: systematic and random.
 The former is not a major concern for detection of differential expression,
 since a 2-fold change in every sample has no effect on the relative fold
 change between samples.
 In contrast, random perturbations would increase the noise and obscure
 the signal in the dataset, reducing the capacity to detect differential
 expression.
\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename graphics/Globin Paper/figure4 - maplot-colored.pdf

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
MA plot showing effects of globin blocking on each gene's abundance.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "fig:MA-plot"

\end_inset


\series bold
MA plot showing effects of globin blocking on each gene's abundance.
 
\series default
All libraries were normalized together as described in Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:logcpm-dists"
plural "false"
caps "false"
noprefix "false"

\end_inset

, and genes with an average logCPM below -1 were filtered out.
 Each remaining gene was tested for differential abundance with respect
 to globin blocking (GB) using edgeR’s quasi-likelihod F-test, fitting a
 negative binomial generalized linear model to table of read counts in each
 library.
 For each gene, edgeR reported average abundance (logCPM), 
\begin_inset Formula $\log_{2}$
\end_inset

 fold change (logFC), p-value, and Benjamini-Hochberg adjusted false discovery
 rate (FDR).
 Each gene's logFC was plotted against its logCPM, colored by FDR.
 Red points are significant at ≤10% FDR, and blue are not significant at
 that threshold.
 The alpha and beta globin genes targeted for blocking are marked with large
 triangles, while all other genes are represented as small points.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
TODO Standardize on 
\begin_inset Quotes eld
\end_inset

log2
\begin_inset Quotes erd
\end_inset

 notation
\end_layout

\end_inset


\end_layout

\begin_layout Standard
The data do indeed show small systematic perturbations in gene levels (Figure
 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:MA-plot"
plural "false"
caps "false"
noprefix "false"

\end_inset

).
 Other than the 3 designated alpha and beta globin genes, two other genes
 stand out as having especially large negative log fold changes: HBD and
 LOC1021365.
 HBD, delta globin, is most likely targeted by the blocking oligos due to
 high sequence homology with the other globin genes.
 LOC1021365 is the aforementioned ncRNA that is reverse-complementary to
 one of the alpha-like genes and that would be expected to be removed during
 the globin blocking step.
 All other genes appear in a cluster centered vertically at 0, and the vast
 majority of genes in this cluster show an absolute log2(FC) of 0.5 or less.
 Nevertheless, many of these small perturbations are still statistically
 significant, indicating that the globin blocking oligos likely cause very
 small but non-zero systematic perturbations in measured gene expression
 levels.
\end_layout

\begin_layout Standard
\begin_inset Float figure
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Graphics
	filename graphics/Globin Paper/figure5 - corrplot.pdf

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status collapsed

\begin_layout Plain Layout
Comparison of inter-sample gene abundance correlations with and without
 globin blocking.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "fig:gene-abundance-correlations"

\end_inset

Comparison of inter-sample gene abundance correlations with and without
 globin blocking (GB).

\series default
 All libraries were normalized together as described in Figure 2, and genes
 with an average abundance (logCPM, log2 counts per million reads counted)
 less than -1 were filtered out.
 Each gene’s logCPM was computed in each library using the edgeR cpm function.
 For each pair of biological samples, the Pearson correlation between those
 samples' GB libraries was plotted against the correlation between the same
 samples’ non-GB libraries.
 Each point represents an unique pair of samples.
 The solid gray line shows a quantile-quantile plot of distribution of GB
 correlations vs.
 that of non-GB correlations.
 The thin dashed line is the identity line, provided for reference.
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
To evaluate the possibility of globin blocking causing random perturbations
 and reducing sample quality, we computed the Pearson correlation between
 logCPM values for every pair of samples with and without GB and plotted
 them against each other (Figure 
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:gene-abundance-correlations"
plural "false"
caps "false"
noprefix "false"

\end_inset

).
 The plot indicated that the GB libraries have higher sample-to-sample correlati
ons than the non-GB libraries.
 Parametric and nonparametric tests for differences between the correlations
 with and without GB both confirmed that this difference was highly significant
 (2-sided paired t-test: t = 37.2, df = 665, P ≪ 2.2e-16; 2-sided Wilcoxon
 sign-rank test: V = 2195, P ≪ 2.2e-16).
 Performing the same tests on the Spearman correlations gave the same conclusion
 (t-test: t = 26.8, df = 665, P ≪ 2.2e-16; sign-rank test: V = 8781, P ≪ 2.2e-16).
 The edgeR package was used to compute the overall biological coefficient
 of variation (BCV) for GB and non-GB libraries, and found that globin blocking
 resulted in a negligible increase in the BCV (0.417 with GB vs.
 0.400 without).
 The near equality of the BCVs for both sets indicates that the higher correlati
ons in the GB libraries are most likely a result of the increased yield
 of useful reads, which reduces the contribution of Poisson counting uncertainty
 to the overall variance of the logCPM values 
\begin_inset CommandInset citation
LatexCommand cite
key "McCarthy2012"
literal "false"

\end_inset

.
 This improves the precision of expression measurements and more than offsets
 the negligible increase in BCV.
\end_layout

\begin_layout Subsection*
More differentially expressed genes are detected with globin blocking
\end_layout

\begin_layout Standard
\begin_inset Float table
wide false
sideways false
status open

\begin_layout Plain Layout
\align center
\begin_inset Tabular
<lyxtabular version="3" rows="5" columns="5">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="1" alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
No Globin Blocking
\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell multicolumn="2" alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
Up
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
NS
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
Down
\end_layout

\end_inset
</cell>
</row>
<row>
<cell multirow="3" alignment="center" valignment="middle" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
Globin-Blocking
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
Up
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\strikeout off
\xout off
\uuline off
\uwave off
\noun off
\color none
231
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
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\color none
515
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
2
\end_layout

\end_inset
</cell>
</row>
<row>
<cell multirow="4" alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
NS
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
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\noun off
\color none
160
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
\size normal
\emph off
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\noun off
\color none
11235
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
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136
\end_layout

\end_inset
</cell>
</row>
<row>
<cell multirow="4" alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\series bold
Down
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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\emph off
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\color none
0
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
\shape up
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548
\end_layout

\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\begin_layout Plain Layout

\family roman
\series medium
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127
\end_layout

\end_inset
</cell>
</row>
</lyxtabular>

\end_inset


\end_layout

\begin_layout Plain Layout
\begin_inset Caption Standard

\begin_layout Plain Layout

\series bold
\begin_inset Argument 1
status open

\begin_layout Plain Layout
Comparison of significantly differentially expressed genes with and without
 globin blocking.
\end_layout

\end_inset


\begin_inset CommandInset label
LatexCommand label
name "tab:Comparison-of-significant"

\end_inset

Comparison of significantly differentially expressed genes with and without
 globin blocking.

\series default
 Up, Down: Genes significantly up/down-regulated in post-transplant samples
 relative to pre-transplant samples, with a false discovery rate of 10%
 or less.
 NS: Non-significant genes (false discovery rate greater than 10%).
\end_layout

\end_inset


\end_layout

\begin_layout Plain Layout

\end_layout

\end_inset


\end_layout

\begin_layout Standard
To compare performance on differential gene expression tests, we took subsets
 of both the GB and non-GB libraries with exactly one pre-transplant and
 one post-transplant sample for each animal that had paired samples available
 for analysis (N=7 animals, N=14 samples in each subset).
 The same test for pre- vs.
 post-transplant differential gene expression was performed on the same
 7 pairs of samples from GB libraries and non-GB libraries, in each case
 using an FDR of 10% as the threshold of significance.
 Out of 12954 genes that passed the detection threshold in both subsets,
 358 were called significantly differentially expressed in the same direction
 in both sets; 1063 were differentially expressed in the GB set only; 296
 were differentially expressed in the non-GB set only; 2 genes were called
 significantly up in the GB set but significantly down in the non-GB set;
 and the remaining 11235 were not called differentially expressed in either
 set.
 These data are summarized in Table 
\begin_inset CommandInset ref
LatexCommand ref
reference "tab:Comparison-of-significant"
plural "false"
caps "false"
noprefix "false"

\end_inset

.
 The differences in BCV calculated by EdgeR for these subsets of samples
 were negligible (BCV = 0.302 for GB and 0.297 for non-GB).
\end_layout

\begin_layout Standard
The key point is that the GB data results in substantially more differentially
 expressed calls than the non-GB data.
 Since there is no gold standard for this dataset, it is impossible to be
 certain whether this is due to under-calling of differential expression
 in the non-GB samples or over-calling in the GB samples.
 However, given that both datasets are derived from the same biological
 samples and have nearly equal BCVs, it is more likely that the larger number
 of DE calls in the GB samples are genuine detections that were enabled
 by the higher sequencing depth and measurement precision of the GB samples.
 Note that the same set of genes was considered in both subsets, so the
 larger number of differentially expressed gene calls in the GB data set
 reflects a greater sensitivity to detect significant differential gene
 expression and not simply the larger total number of detected genes in
 GB samples described earlier.
\end_layout

\begin_layout Section
Discussion
\end_layout

\begin_layout Standard
The original experience with whole blood gene expression profiling on DNA
 microarrays demonstrated that the high concentration of globin transcripts
 reduced the sensitivity to detect genes with relatively low expression
 levels, in effect, significantly reducing the sensitivity.
 To address this limitation, commercial protocols for globin reduction were
 developed based on strategies to block globin transcript amplification
 during labeling or physically removing globin transcripts by affinity bead
 methods 
\begin_inset CommandInset citation
LatexCommand cite
key "Winn2010"
literal "false"

\end_inset

.
 More recently, using the latest generation of labeling protocols and arrays,
 it was determined that globin reduction was no longer necessary to obtain
 sufficient sensitivity to detect differential transcript expression 
\begin_inset CommandInset citation
LatexCommand cite
key "NuGEN2010"
literal "false"

\end_inset

.
 However, we are not aware of any publications using these currently available
 protocols the with latest generation of microarrays that actually compare
 the detection sensitivity with and without globin reduction.
 However, in practice this has now been adopted generally primarily driven
 by concerns for cost control.
 The main objective of our work was to directly test the impact of globin
 gene transcripts and a new globin blocking protocol for application to
 the newest generation of differential gene expression profiling determined
 using next generation sequencing.
 
\end_layout

\begin_layout Standard
The challenge of doing global gene expression profiling in cynomolgus monkeys
 is that the current available arrays were never designed to comprehensively
 cover this genome and have not been updated since the first assemblies
 of the cynomolgus genome were published.
 Therefore, we determined that the best strategy for peripheral blood profiling
 was to do deep RNA-seq and inform the workflow using the latest available
 genome assembly and annotation 
\begin_inset CommandInset citation
LatexCommand cite
key "Wilson2013"
literal "false"

\end_inset

.
 However, it was not immediately clear whether globin reduction was necessary
 for RNA-seq or how much improvement in efficiency or sensitivity to detect
 differential gene expression would be achieved for the added cost and work.
 
\end_layout

\begin_layout Standard
We only found one report that demonstrated that globin reduction significantly
 improved the effective read yields for sequencing of human peripheral blood
 cell RNA using a DeepSAGE protocol 
\begin_inset CommandInset citation
LatexCommand cite
key "Mastrokolias2012"
literal "false"

\end_inset

.
 The approach to DeepSAGE involves two different restriction enzymes that
 purify and then tag small fragments of transcripts at specific locations
 and thus, significantly reduces the complexity of the transcriptome.
 Therefore, we could not determine how DeepSAGE results would translate
 to the common strategy in the field for assaying the entire transcript
 population by whole-transcriptome 3’-end RNA-seq.
 Furthermore, if globin reduction is necessary, we also needed a globin
 reduction method specific to cynomolgus globin sequences that would work
 an organism for which no kit is available off the shelf.
\end_layout

\begin_layout Standard
As mentioned above, the addition of globin blocking oligos has a very small
 impact on measured expression levels of gene expression.
 However, this is a non-issue for the purposes of differential expression
 testing, since a systematic change in a gene in all samples does not affect
 relative expression levels between samples.
 However, we must acknowledge that simple comparisons of gene expression
 data obtained by GB and non-GB protocols are not possible without additional
 normalization.
 
\end_layout

\begin_layout Standard
More importantly, globin blocking not only nearly doubles the yield of usable
 reads, it also increases inter-sample correlation and sensitivity to detect
 differential gene expression relative to the same set of samples profiled
 without blocking.
 In addition, globin blocking does not add a significant amount of random
 noise to the data.
 Globin blocking thus represents a cost-effective way to squeeze more data
 and statistical power out of the same blood samples and the same amount
 of sequencing.
 In conclusion, globin reduction greatly increases the yield of useful RNA-seq
 reads mapping to the rest of the genome, with minimal perturbations in
 the relative levels of non-globin genes.
 Based on these results, globin transcript reduction using sequence-specific,
 complementary blocking oligonucleotides is recommended for all deep RNA-seq
 of cynomolgus and other nonhuman primate blood samples.
\end_layout

\begin_layout Chapter
Future Directions
\end_layout

\begin_layout Itemize
Study other epigenetic marks in more contexts
\end_layout

\begin_deeper
\begin_layout Itemize
DNA methylation, histone marks, chromatin accessibility & conformation in
 CD4 T-cells
\end_layout

\begin_layout Itemize
Also look at other types lymphocytes: CD8 T-cells, B-cells, NK cells
\end_layout

\end_deeper
\begin_layout Itemize
Investigate epigenetic regulation of lifespan extension in 
\emph on
C.
 elegans
\end_layout

\begin_deeper
\begin_layout Itemize
ChIP-seq of important transcriptional regulators to see how transcriptional
 drift is prevented
\end_layout

\end_deeper
\begin_layout Standard
\begin_inset ERT
status open

\begin_layout Plain Layout

% Use "References" instead of "Bibliography" 
\end_layout

\begin_layout Plain Layout


\backslash
renewcommand{
\backslash
bibname}{References}
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset Note Note
status open

\begin_layout Plain Layout
TODO: Check bib entry formatting & sort order
\end_layout

\end_inset


\end_layout

\begin_layout Standard
\begin_inset CommandInset bibtex
LatexCommand bibtex
btprint "btPrintCited"
bibfiles "refs"
options "plain"

\end_inset


\end_layout

\end_body
\end_document