-
Notifications
You must be signed in to change notification settings - Fork 0
/
appendix_thirdpartydata.tex
65 lines (50 loc) · 4.02 KB
/
appendix_thirdpartydata.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
\chapter{Sources of reanalyzed third-party datasets}
\label{chap:ap:thirdpartydata}
\section*{ATAC-seq}
\label{chap:ap:thirdpartydata:atac}
\begin{tabular}{ll>{\raggedright}p{7.5cm}p{3.0cm}}
\textbf{Source} & \textbf{Identifier} & \textbf{Data type} & \textbf{referred at} \\
\hline
\cite{Lara-Astiaso2014} & GSM1463173 & ATAC-seq profile of granulocyte-macrophage progenitors as healthy control sample & Pages \pageref{chap:r:enhancers:trowbridgestart}-\pageref{chap:r:enhancers:trowbridgeend} \\
\cite{George2016} & GSE74688 & Profiles of \mllafnine bulk AML samples & Pages \pageref{chap:r:enhancers:trowbridgestart}-\pageref{chap:r:enhancers:trowbridgeend} \\
\cite{George2016} & GSE81805 & Profiles of \mllafnine L-GMP samples & Pages \pageref{chap:r:enhancers:trowbridgestart}-\pageref{chap:r:enhancers:trowbridgeend} \\
\end{tabular}
\section*{ChIP-seq}
\label{chap:ap:thirdpartydata:chip}
\begin{tabular}{ll>{\raggedright}p{7.5cm}p{3.0cm}}
\textbf{Source} & \textbf{Identifier} & \textbf{Data type} & \textbf{referred at} \\
\hline
\cite{Bernt2011} & GSE29130 & \hisfourthree, \histwentyseventhree, \histhirtysixthree and \hisseventyninetwo as well as \mllafnine ChIP-seq from HSCs, \mllafnine \kithi + \kitlow & Page \pageref{chap:r:enhancers:motifs:berntcite}\\
\cite{Lara-Astiaso2014} & GSE60103 & \hisfourone, \hisfourtwo, \hisfourthree and \histwentysevenac ChIP-seq from healthy hematopoietic cells & Pages \pageref{chap:r:enhancers:cluster}-\pageref{chap:r:enhancers:amitend} \\
\cite{Wong2015} & GSE60193 & \hisfourtwo, \hisfourthree , \hiseighteenac, \histwentysevenac, \histwentyseventhree, \histhirtysixthree, \hisseventyninetwo and \poltwo ChIP-seqs from \mllafnine \kithi as well as \kitlow cells & Pages \pageref{chap:r:enhancers:cluster:clades:clearydata}-\pageref{chap:r:enhancers:clearyend} \\
\cite{Hu2017} & GSE78708 &\proteinnamemouse{Mll2}, \proteinnamemouse{Menin} and \hisfourthree ChIP-seq from murine embryonal stem cells (cell line V6.5) & Pages \pageref{chap:r:enhancers:motifs:mlltwo}-\pageref{chap:r:enhancers:motifs:summary} \\
\end{tabular}
\section*{Hi-C}
\label{chap:ap:thirdpartydata:hic}
\begin{tabular}{ll>{\raggedright}p{7.3cm}p{2cm}}
\textbf{Source} & \textbf{Identifier} & \textbf{Data type} & \textbf{referred at} \\
\hline
\cite{Wilson2016} & E-MTAB-3954 & Hi-C and Capture Hi-C in HPC-7 cells & \raggedright Pages \pageref{chap:r:gam:chromatin:hic}, \pageref{fig:tinatdensplot_LSChicpc1overall.pdf}, \pageref{chap:r:enhancers:targets:assignment} \\
\end{tabular}
\section*{RNA-seq}
\label{chap:ap:thirdpartydata:rna}
\begin{tabular}{llp{7.5cm}p{3.0cm}}
\textbf{Source} & \textbf{Identifier} & \textbf{Data type} & \textbf{referred at} \\
\hline
%\cite{Delconte2016} & GSE76466 & RNA-seq of NK cells & d \\
\cite{Chen2017a} & GSE93622 & RNA-seq of \mllafnine-transformed \kitpos bone marrow cells. Either \proteinnamemouse{Mll1}, \proteinnamemouse{Mll2} or both were deleted & \raggedright Page \pageref{chap:r:enhancers:targets:mlltwotargets} \\
\end{tabular}
\section*{WGBS}
\label{chap:ap:thirdpartydata:wgbs}
\begin{tabular}{llp{7.5cm}p{3.0cm}}
\textbf{Source} & \textbf{Identifier} & \textbf{Data type} & \textbf{referred at} \\
\hline
\cite{Jeong2014} & GSE49714 & Bisulfite sequencing of secondarily transplanted wild-type hematopoietic stem cells & \raggedright Pages \pageref{chap:r:wgbs:demethylation}-\pageref{fig:wgbs_gam_points_chr18.pdf}, \pageref{chap:r:enhancers:motifs:methylation:motifs}-\pageref{chap:r:enhancers:motifs:mlltwo} \\
\end{tabular}
%Gene Expression Omnibus
%GSE84238 \hisfourthree, \histwentyseventhree and \histwentysevenac ChIP-seqs and ATAC-seq from iNKT cells\cite{Beyaz2017}
%GSE78708 MLL2 and \hisfourthree ChIP-seqs from ES cells \cite{Hu}
%GSE93622 RNA-seq from MLL-2 and MLL-1 deficient MLL-AF9-transformed cells\cite{Chen2017a}
%GSE104307 ChIP-seq for TAF2,TAF10 and TAF12 in murine MLL-AF9/NrasG12D AML \cite{Xu2018}
%GSE97462 - other NK cell RNAseq dataset
%Gene Expression Omnibus GSE98140 \cite{Cao2017}: ChiP-seq an RNA-seq of Hox cluster shadow enhancers