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Series GSE136692 Query DataSets for GSE136692
Status Public on Jun 16, 2023
Title ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The lineage-determining transcription factor ETV2 is necessary and sufficient for hematoendothelial fate commitment. We investigated how ETV2-driven gene regulatory networks promote hematoendothelial fate commitment. We resolved the sequential determination steps of hematoendothelial versus cardiac differentiation from mouse embryonic stem cells. Etv2 was strongly induced and bound to the enhancers of hematoendothelial genes in a common cardiomyocyte-hematoendothelial mesoderm progenitor. However, only Etv2 itself and Tal1, not other ETV2-bound genes, were induced. Despite ETV2 genomic binding and Etv2 and Tal1 expression, cardiomyogenic fate potential was maintained. A second wave of ETV2-bound target genes was up-regulated during the transition from the common cardiomyocyte-hematoendothelial progenitor to the committed hematoendothelial population. A third wave of ETV-bound genes were subsequently expressed in the committed hematoendothelial population for sub-lineage differentiation. The shift from ETV2 binding to productive transcription, not ETV2 binding to target gene enhancers, drove hematoendothelial fate commitment. This work identifies mechanistic phases of ETV2-dependent gene expression that distinguish hematoendothelial specification, commitment, and differentiation.
Overall design For ATAC-seq, there are 37 samples:
3 each of Day 0, Day 2, Day 4 P+F-, Day 4 P+F+, Day 4 P-F+, Day 6 P+F+, Day 6 P-F+, Day 8 P+F+, and Day 8 P-F+;
4 Day 4 P+F+ under FAB conditions;
2 Day 4 P+F+ under FAB+V conditions; and
4 Day 4 P+F+ under FAB+P conditions.

For RNA-seq, there are 14 samples under the FAB+V conditions:
3 Day 4 P+F-, 2 Day 4 P+F+, 3 Day 4 P-F+, 3 Day 8 P+F+, and 3 Day 8 P-F+.

Under differing conditions, all P+F+, there are 23 samples:
3 Day 4 FAB, 3 Day 4 FAB+P, 3 Day 4 FAB+V, 3 Day 6 FAB, 2 Day 6 FAB+P, 2 Day 6 FAB+V, 3 Day 8 FAB, 2 Day 8 FAB+P, and 2 Day 8 FAB+V.

For ChIP-seq, there are 9 samples labelled as H3K27ac or Input controls with 2 replicates Day 4 P+F+ under FAB+V, 2 replicates Day 4 P+F+ under FAB, 2 replicates at Day 5 under FAB+V, or 1 replicate of each input.

Treatment definitions:
FAB: bFGF+Activin A+BMP4
Contributor(s) Steimle JD, Kim C, Moskowitz IP, Ikegami K
Citation(s) 37330911
Submission date Aug 30, 2019
Last update date Sep 15, 2023
Contact name Jeffrey D. Steimle
Phone 7137985917
Organization name Baylor College of Medicine
Department Molecular Physiology and Biophysics
Lab Room 504E, Mail Stop BCM335
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (83)
GSM4055326 RNA-seq_Day4_AABMP4_1
GSM4055327 RNA-seq_Day4_AABMP4_2
GSM4055328 RNA-seq_Day4_AABMP4_3
BioProject PRJNA563075
SRA SRP219954

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 6.3 Gb (ftp)(http) TAR
GSE136692_Combined_ATAC_summits.bed.tar.gz 12.8 Mb (ftp)(http) TAR 475.7 Mb (ftp)(http) BW
GSE136692_K27ac_D4PF_ABV_macs2mm10_t948t949c965_peaks.narrowPeak.gz 364.3 Kb (ftp)(http) NARROWPEAK 518.4 Mb (ftp)(http) BW
GSE136692_K27ac_D4PF_AB_macs2mm10_t950t951c966_peaks_fe5.narrowPeak.gz 150.3 Kb (ftp)(http) NARROWPEAK 334.0 Mb (ftp)(http) BW
GSE136692_K27ac_D5F_ABV_macs2mm10_t954t955c968_peaks_fe5.narrowPeak.gz 388.9 Kb (ftp)(http) NARROWPEAK
GSE136692_RAW.tar 8.1 Gb (http)(custom) TAR (of BED, BW)
GSE136692_RNAseq_Compilation.txt.gz 5.7 Mb (ftp)(http) TXT
GSE136692_UnifiedATAC_Dataset.txt.gz 65.8 Mb (ftp)(http) TXT
GSE136692_edgeR_Results_FABVoverFAB.txt.gz 3.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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