|
| Status |
Public on Jun 26, 2024 |
| Title |
Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE
|
| |
|
| Overall design |
EpiSCs were converted to DE and live cells isolated by flow cytometry. OTX2 binding sites were mapped in mouse EpiSCs and definitive endoderm using CUT&RUN for HA in OTX2-HA tagged cell lines.
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| |
|
| Contributor(s) |
Stadtfeld M, Ee L, Medina-Cano D, Polyzos A |
| Citation(s) |
38854146 |
| |
| Submission date |
Jan 30, 2024 |
| Last update date |
Mar 24, 2025 |
| Contact name |
Ly-sha Ee |
| E-mail(s) |
lye4001@med.cornell.edu, worms917@yahoo.com
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
413 E 69th Street
|
| City |
New York |
| ZIP/Postal code |
100021 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA1071101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE254590_CnR_DE_MERGE.bw |
130.6 Mb |
(ftp)(http) |
BW |
| GSE254590_CnR_EpiSCs_MERGE.bw |
182.5 Mb |
(ftp)(http) |
BW |
| GSE254590_DE_CnR_Peaks_merge50bp.bed.gz |
336.8 Kb |
(ftp)(http) |
BED |
| GSE254590_EpiSCs_CnR_Peaks_merge50bp.bed.gz |
52.5 Kb |
(ftp)(http) |
BED |
| GSE254590_OTX2_DE_HApeaks.txt.gz |
446.4 Kb |
(ftp)(http) |
TXT |
| GSE254590_OTX2_Epi_HApeaks.txt.gz |
78.3 Kb |
(ftp)(http) |
TXT |
| GSE254590_OTX2_Epi_IgGpeaks_Rep1.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
| GSE254590_OTX2_Epi_IgGpeaks_Rep2.txt.gz |
1.3 Kb |
(ftp)(http) |
TXT |
| GSE254590_OTX2_Epi_IgGpeaks_Rep3.txt.gz |
1.7 Kb |
(ftp)(http) |
TXT |
| GSE254590_wt_de1_noTrt_aHA_rep1_mm10_trim_q5_dupsRem_20to120_peaks.narrowPeak.gz |
623 b |
(ftp)(http) |
NARROWPEAK |
| GSE254590_wt_de1_noTrt_aHA_rep1_mm10_trim_q5_dupsRem_20to120_rpgcNorm.bw |
121.3 Mb |
(ftp)(http) |
BW |
| GSE254590_wt_de1_noTrt_aIgG_rep1_mm10_trim_q5_dupsRem_20to120_rpgcNorm.bw |
95.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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