 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 16, 2024 |
| Title |
Defining key transcriptional regulators of extravillous trophoblast differentiation [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
During early human pregnancy, extravillous trophoblasts (EVT) play a central role in placental anchorage and blood vessel remodeling. Despite the essential roles in pregnancy, key factors and mechanisms underlying EVT differentiation remain largely unknown. Here, we defined key transcription factors (TFs) by monitoring the dynamics of transcriptome and enhancer usage during EVT differentiation. We confirmed the requirements of the defined TFs and identified their action mechanisms.
|
| |
|
| Overall design |
ChIP-seq of H3K27ac was performed in human trophoblast stem cells (TSC), EVT differentiating cells (day 3, EVT D3), and fully differentiated EVT (day 8, EVT D8). ATAC-seq and H3K4me3 ChIP-seq were performed in TSC and EVT D8. Time-course ChIP-seq of TFAP2C and DLX6 were performed in TSC, EVT D2, EVT D5, and EVT D8. To map genomic targets of DLX5 and ASCL2, ChIP-seq using native antibodies was conducted, and NRIP1 targets were identified by biotin-mediated ChIP-seq (bioChIP-seq). Inputs were sequenced for a control.
|
| |
|
| Contributor(s) |
Kim J, Kim M |
| Citation(s) |
38346993 |
| |
| Submission date |
Aug 29, 2022 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Mijeong Kim |
| E-mail(s) |
mjkim@utexas.edu
|
| Organization name |
The University of Texas at Austin
|
| Street address |
2506 Speedway, NMS 4.246
|
| City |
Austin |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (46)
|
| GSM6522552 |
EVT_D3, H3K27ac, ChIP-seq, rep2 |
| GSM6522553 |
EVT_D3, H3K27ac, ChIP-seq, rep3 |
| GSM6522554 |
EVT_D8, H3K27ac, ChIP-seq, rep1 |
| GSM6522556 |
EVT_D8, H3K27ac, ChIP-seq, rep2 |
| GSM6522557 |
EVT_D8, H3K27ac, ChIP-seq, rep3 |
| GSM6522558 |
TSC, H3K4me3, ChIP-seq |
| GSM6522559 |
EVT_D8, H3K4me3, ChIP-seq |
| GSM6522560 |
TSC, ATAC-seq |
| GSM6522562 |
EVT_D8, ATAC-seq |
| GSM6522563 |
EVT_D2, TFAP2C, ChIP-seq |
| GSM6522564 |
EVT_D5, TFAP2C, ChIP-seq |
| GSM6522565 |
EVT_D8, TFAP2C, ChIP-seq |
| GSM6522566 |
TSC, DLX6, ChIP-seq |
| GSM6522567 |
EVT_D2, DLX6, ChIP-seq |
| GSM6522569 |
EVT_D5, DLX6, ChIP-seq |
| GSM6522570 |
EVT_D8, DLX6, ChIP-seq, rep1 |
| GSM6522571 |
EVT_D8, DLX6, ChIP-seq, rep2 |
| GSM6522572 |
EVT_D8, ASCL2, ChIP-seq, rep1 |
| GSM6522573 |
EVT_D8, ASCL2, ChIP-seq, rep2 |
| GSM6522574 |
EVT_D8, DLX5, ChIP-seq, rep1 |
| GSM6522576 |
EVT_D8, DLX5, ChIP-seq, rep2 |
| GSM6522577 |
EVT_D8, NRIP1, bioChIP-seq |
| GSM6522578 |
TSC, Input |
| GSM6522579 |
EVT_D3, Input |
| GSM6522580 |
EVT_D8, Input |
| GSM7596507 |
TSC, P300, ChIP-seq, rep1 |
| GSM7596508 |
TSC, P300, ChIP-seq, rep2 |
| GSM7596509 |
EVT_D3, P300, ChIP-seq, rep1 |
| GSM7596510 |
EVT_D3, P300, ChIP-seq, rep2 |
| GSM7596511 |
EVT_D8, P300, ChIP-seq, rep1 |
| GSM7596512 |
EVT_D8, P300, ChIP-seq, rep2 |
| GSM7596513 |
TSC, Med1, ChIP-seq, rep1 |
| GSM7596514 |
TSC, Med1, ChIP-seq, rep2 |
| GSM7596515 |
EVT_D3, Med1, ChIP-seq, rep1 |
| GSM7596516 |
EVT_D3, Med1, ChIP-seq, rep2 |
| GSM7596517 |
EVT_D8, Med1, ChIP-seq, rep1 |
| GSM7596518 |
EVT_D8, Med1, ChIP-seq, rep2 |
| GSM7596519 |
TSC, H3K4me1, ChIP-seq, rep1 |
| GSM7596520 |
TSC, H3K4me1, ChIP-seq, rep2 |
| GSM7596521 |
EVT_D3, H3K4me1, ChIP-seq, rep1 |
| GSM7596522 |
EVT_D3, H3K4me1, ChIP-seq, rep2 |
| GSM7596523 |
EVT_D8, H3K4me1, ChIP-seq, rep1 |
| GSM7596524 |
EVT_D8, H3K4me1, ChIP-seq, rep2 |
|
| This SubSeries is part of SuperSeries: |
| GSE212267 |
Defining key transcriptional regulators of extravillous trophoblast differentiation |
|
| Relations |
| BioProject |
PRJNA874728 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE212265_ASCL2_EVT_D8_comb.peak.txt.gz |
77.7 Kb |
(ftp)(http) |
TXT |
| GSE212265_ATAC_EVT_D8.peak.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE212265_ATAC_TSC.peak.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE212265_DLX5_EVT_D8_comb.peak.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE212265_DLX6_EVT_D2.peak.txt.gz |
|
(ftp)(http) |
TXT |
| GSE212265_DLX6_EVT_D5.peak.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE212265_DLX6_EVT_D8_comb.peak.txt.gz |
1020.6 Kb |
(ftp)(http) |
TXT |
| GSE212265_DLX6_TSC.peak.txt.gz |
96 b |
(ftp)(http) |
TXT |
| GSE212265_EVT3D_H3K4me1_comb.final.peak.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
| GSE212265_EVT3D_Med1_comb.final.peak.txt.gz |
713.2 Kb |
(ftp)(http) |
TXT |
| GSE212265_EVT3D_P300_comb.final.peak.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
| GSE212265_EVT8D_H3K4me1_comb.final.peak.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSE212265_EVT8D_Med1_comb.final.peak.txt.gz |
287.6 Kb |
(ftp)(http) |
TXT |
| GSE212265_EVT8D_P300_comb.final.peak.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| GSE212265_H3K27ac_EVT_D3_comb.peak.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE212265_H3K27ac_EVT_D8_comb.peak.txt.gz |
1016.0 Kb |
(ftp)(http) |
TXT |
| GSE212265_H3K27ac_TSC_comb.peak.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE212265_H3K4me3_EVT_D8.peak.txt.gz |
743.9 Kb |
(ftp)(http) |
TXT |
| GSE212265_H3K4me3_TSC.peak.txt.gz |
967.3 Kb |
(ftp)(http) |
TXT |
| GSE212265_NRIP1_EVT_D8.peak.txt.gz |
120.1 Kb |
(ftp)(http) |
TXT |
| GSE212265_TFAP2C_EVT_D2.peak.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE212265_TFAP2C_EVT_D5.peak.txt.gz |
88.6 Kb |
(ftp)(http) |
TXT |
| GSE212265_TFAP2C_EVT_D8.peak.txt.gz |
59.3 Kb |
(ftp)(http) |
TXT |
| GSE212265_TSC_H3K4me1_comb.final.peak.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
| GSE212265_TSC_Med1_comb.final.peak.txt.gz |
269.3 Kb |
(ftp)(http) |
TXT |
| GSE212265_TSC_P300_comb.final.peak.txt.gz |
977.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...