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Status |
Public on Jun 26, 2024 |
Title |
OTX2-dTAG_DE_ATAC_DMSO_Rep3 |
Sample type |
SRA |
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Source name |
7H OTX2-dTAG-EGFP
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Organism |
Mus musculus |
Characteristics |
cell line: 7H OTX2-dTAG-EGFP cell type: Definitive Endoderm strain: BL6/129 hybrid treatment: DMSO
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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
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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
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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)
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
ATAC_DE_allpeaks.txt DMSO_ALL.bw DMSO_ALL.mm10.macs2_peaks.bed ATAC_DE_DMSOenrich_peaks.txt ATAC_DE_dTAGenrich_peaks.txt
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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
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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] |
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Relations |
BioSample |
SAMN39649602 |
SRA |
SRX23448218 |