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Series GSE254590 Query DataSets for GSE254590
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.
 
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)
GSM8046718 OTX2-dTAG_EpiSC_IgG_Rep1
GSM8046719 OTX2-dTAG_EpiSC_IgG_Rep2
GSM8046720 OTX2-dTAG_EpiSC_IgG_Rep3
Relations
BioProject PRJNA1071101

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
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
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