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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
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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
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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 |
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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
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Organization name |
Weill Cornell Medicine
|
Street address |
413 E 69th Street
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City |
New York |
ZIP/Postal code |
100021 |
Country |
USA |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (10)
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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 |