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@@ -3416,7 +3416,26 @@ RNA-seq
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\end_inset
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- data from previous studies
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+ data from previous studies (
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+\begin_inset Flex Glossary Term
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+status open
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+
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+\begin_layout Plain Layout
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+GEO
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+\end_layout
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+
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+\end_inset
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+
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+ accession number
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+\begin_inset CommandInset href
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+LatexCommand href
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+name "GSE73214"
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+target "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73214"
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+literal "false"
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+
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+\end_inset
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+
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+)
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\begin_inset CommandInset citation
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LatexCommand cite
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key "gh-cd4-csaw,LaMere2016,LaMere2017"
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@@ -3806,7 +3825,7 @@ literal "false"
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some of the batch effect in the data
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\begin_inset CommandInset citation
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LatexCommand cite
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-key "gh-shoal,Patro2017"
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+key "Patro2017,gh-shoal"
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literal "false"
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\end_inset
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@@ -7100,7 +7119,7 @@ noprefix "false"
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t
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\emph default
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-test, all
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-\begin_inset Formula $p\mathrm{-values}\ll2.2\times10^{-16}$
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+\begin_inset Formula $p\textrm{-values}\ll2.2\times10^{-16}$
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\end_inset
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).
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@@ -8137,8 +8156,8 @@ end{landscape}
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\end_layout
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\begin_layout Subsection
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-Effect of H3K4me2 and H3K4me3 promoter coverage upstream vs downstream of
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- TSS
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+Effect of resting H3K4me2 and H3K4me3 promoter coverage landscapes on gene
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+ expression
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\end_layout
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\begin_layout Standard
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@@ -9095,7 +9114,7 @@ end{landscape}
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\end_layout
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\begin_layout Subsection
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-Promoter coverage H3K27me3
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+Effect of resting H3K27me3 promoter coverage landscapes on gene expression
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\end_layout
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\begin_layout Standard
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@@ -9574,6 +9593,10 @@ TSS
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\end_layout
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\begin_layout Standard
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+\begin_inset Note Note
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+status open
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+
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+\begin_layout Plain Layout
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\begin_inset Flex TODO Note (inline)
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status open
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@@ -9591,7 +9614,7 @@ Show the figures where the negative result ended this line of inquiry.
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Defined pattern analysis
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\end_layout
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-\begin_layout Standard
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+\begin_layout Plain Layout
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\begin_inset Flex TODO Note (inline)
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status open
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@@ -9612,9 +9635,9 @@ This was where I defined interesting expression patterns and then looked
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Promoter CpG islands?
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\end_layout
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-\begin_layout Standard
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+\begin_layout Plain Layout
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\begin_inset Flex TODO Note (inline)
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-status collapsed
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+status open
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\begin_layout Plain Layout
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I forgot until recently about the work I did on this.
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@@ -9624,6 +9647,11 @@ I forgot until recently about the work I did on this.
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\end_inset
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+\end_layout
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+
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+\end_inset
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+
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+
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\end_layout
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\begin_layout Section
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@@ -9819,7 +9847,7 @@ kb radius determined from TSS-to-peak distances is functionally significant.
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\end_layout
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\begin_layout Subsection
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-Convergence
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+Day 14 convergence is consistent with naïve-to-memory differentiation
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\end_layout
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\begin_layout Standard
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@@ -10136,7 +10164,7 @@ Model for the role of H3K4 methylation during CD4
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\end_layout
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\begin_layout Subsection
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-Positional
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+The location of histone modifications within the promoter is important
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\end_layout
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\begin_layout Standard
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@@ -10316,7 +10344,7 @@ TSS
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\end_layout
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\begin_layout Subsection
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-Workflow
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+A reproducible workflow aids in analysis
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\end_layout
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\begin_layout Standard
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@@ -10670,7 +10698,7 @@ ChIP-seq
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\end_layout
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\begin_layout Subsection
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-Negative results
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+Previous negative results
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\end_layout
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\begin_layout Standard
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