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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| 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
FAB+P: bFGF+Activin A+BMP4+PDGFAA
FAB+V: bFGF+Activin A+BMP4+VEGF
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| Contributor(s) |
Steimle JD, Kim C, Moskowitz IP, Ikegami K |
| Citation(s) |
37330911 |
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| Submission date |
Aug 30, 2019 |
| Last update date |
Jan 17, 2024 |
| Contact name |
Jeffrey D. Steimle |
| E-mail(s) |
[email protected], [email protected], [email protected]
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| Phone |
7137985917
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular Physiology and Biophysics
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| Lab |
Room 504E, Mail Stop BCM335
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (83)
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| Relations |
| BioProject |
PRJNA563075 |
| SRA |
SRP219954 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136692_Combined_ATAC.bw.tar.gz |
6.3 Gb |
(ftp)(http) |
TAR |
| GSE136692_Combined_ATAC_summits.bed.tar.gz |
12.8 Mb |
(ftp)(http) |
TAR |
| GSE136692_K27ac_D4PF_ABV_macs2mm10_t948t949c965_fe_k1sort.bw |
475.7 Mb |
(ftp)(http) |
BW |
| GSE136692_K27ac_D4PF_ABV_macs2mm10_t948t949c965_peaks.narrowPeak.gz |
364.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE136692_K27ac_D4PF_AB_macs2mm10_t950t951c966_fe_k1sort.bw |
518.4 Mb |
(ftp)(http) |
BW |
| GSE136692_K27ac_D4PF_AB_macs2mm10_t950t951c966_peaks_fe5.narrowPeak.gz |
150.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE136692_K27ac_D5F_ABV_macs2mm10_t954t955c968_fe_k1sort.bw |
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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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