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Series GSE115045 Query DataSets for GSE115045
Status Public on Oct 23, 2019
Title Massively parallel characterization of regulatory dynamics during neural induction [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (21)
GSM3163888 RNAseq_0hr_rep1
GSM3163889 RNAseq_3hr_rep1
GSM3163890 RNAseq_6hr_rep1
This SubSeries is part of SuperSeries:
GSE115046 Massively parallel characterization of regulatory dynamics during neural induction
Relations
BioProject PRJNA473883
SRA SRP149491

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Supplementary file Size Download File type/resource
GSE115045_tophat2_featureCountsTable.txt.gz 1.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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