NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8042168 Query DataSets for GSM8042168
Status Public on Jun 26, 2024
Title OTX2-dTAG_DE_ATAC_dTAG_Rep1
Sample type SRA
 
Source name 7H OTX2-dTAG-EGFP
Organism Mus musculus
Characteristics cell line: 7H OTX2-dTAG-EGFP
cell type: Definitive Endoderm
strain: BL6/129 hybrid
treatment: dTAG13
Treatment protocol dTAG13 or DMSO vehicle added at primitive streak (PS) stage for 24hrs to deplete OTX2. Live DE cells were sorted for ATACseq with DAPI on BD-Influx
Growth protocol All cells cultured at 37C, 5% CO2. DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs followed by 100ng/ml Activin A, 100nM LDN for 24hrs
Extracted molecule genomic DNA
Extraction protocol ATACseq was performed on 50,000 DE cells per sample using the Nextera DNA library preparation kit (Illumina FC121103) according to the manufacturer's instructions
Libraries were constructed using the Nextera DNA library preparation kit (Illumina FC121103) and NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) according to the manufacturer's instructions. Cycles for PCR amplification were determined individually for each sample by qPCR Libraries were size selected (0.55–1.5x) using SPRI beads (Beckman Coulter)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description ATAC_DE_allpeaks.txt
dTAG_ALL.bw
dTAG_ALL.mm10.macs2_peaks.bed
ATAC_DE_DMSOenrich_peaks.txt
ATAC_DE_dTAGenrich_peaks.txt
Data processing Raw ATAC-seq reads were trimmed using fastp to remove low-quality bases from reads (quality<20) and adapter sequences. The trimmed reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) to UCSC genome assembly mm10. Duplicate reads were removed using Sambamba.
Peaks were identified with MACS2 (Gaspar, 2018) and those overlapping with satellite repeat regions were discarded.
Peak intensity for each sample was counted using featureCounts (Liao, et al., 2014). HOMER (v4.11) (Heinz, et al., 2010) was used for motif analyses. To associate peaks with nearby genes and genomic location, ChipSeeker (Yu, et al., 2015) was used
For further analyses, a union peak atlas was created from the MACS2 files
Assembly: mm10
Supplementary files format and content: BigWig, bed
Supplementary files format and content: txt
 
Submission date Jan 29, 2024
Last update date Jun 26, 2024
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
 
Platform ID GPL24247
Series (1)
GSE254431 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]
Relations
BioSample SAMN39649601
SRA SRX23448219

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap