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Series GSE115042 Query DataSets for GSE115042
Status Public on Oct 23, 2019
Title Massively parallel characterization of regulatory dynamics during neural induction [MPRA]
Organism Homo sapiens
Experiment type Other
Summary The molecular components governing neural induction remain largely unknown. Here, we used a suite of genomic and computational tools to comprehensively identify these components. We performed RNA-seq, ChIP-seq (H3K27ac, H3K27me3) and ATAC-seq on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours) and identified thousands of induced genes and their putative regulatory regions. We analyzed the function of ~2,500 selected regions using massively parallel reporter assays at all time points. We found numerous temporal enhancers that correlated with similarly timed epigenetic marks and gene expression. Development of a prioritization method that incorporated all genomic data identified key transcription factors (TFs) involved in neural induction. Individual overexpression of eleven TFs and several combinations in hESCs found novel neural induction regulators. Combined, our results provide a comprehensive map of genes and functional regulatory elements involved in neural induction and identify master regulator TFs that are instrumental for this process.
 
Overall design RNA-seq (3 replicates), ChIP-seq (H3K27ac, H3K27me3 - 2 replicates) and ATAC-seq (2 replicates) were preformed on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours). Additionally, the function of ~2,500 selected regions was analyzed using massively parallel reporter assays at all time points (3 replicates).
 
Contributor(s) Inoue F, Kreimer A, Ahituv N, Yosef N
Citation(s) 31631012, 38296821
Submission date May 29, 2018
Last update date Mar 20, 2024
Contact name Anat Kreimer
E-mail(s) anat.kreimer@berkeley.edu
Organization name University of California, Berkeley
Street address 378 Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (3)
GSM3163823 MPRA_rep1
GSM3163824 MPRA_rep2
GSM3163825 MPRA_rep3
This SubSeries is part of SuperSeries:
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
Relations
BioProject PRJNA474066
SRA SRP149726

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Supplementary file Size Download File type/resource
GSE115042_MPRA.tar.gz 166.0 Mb (ftp)(http) TAR
GSE115042_experimental_design.txt.gz 437 b (ftp)(http) TXT
GSE115042_index_rep1.lst.txt.gz 190 b (ftp)(http) TXT
GSE115042_index_rep2.lst.txt.gz 192 b (ftp)(http) TXT
GSE115042_index_rep3.lst.txt.gz 191 b (ftp)(http) TXT
GSE115042_plasmid_library_MPRA.fa.gz 3.2 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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