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Sample GSM6829373

Query DataSets for GSM6829373

Status

Public on Jul 20, 2023

Title

bTSC_2_ATACseq

Sample type

SRA

Source name

Embryonic cells

Organism

Bos taurus

Characteristics

cell type: trophoblast stem cells (TSCs)

Extracted molecule

genomic DNA

Extraction protocol

Not provided

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

Description

bTSC_2

Data processing

All quality assessed ATAC-seq reads were aligned to the bovine reference genome using Bowtie 2.3 with following options: –very-sensitive -X 2000 –no-mixed –no-discordant. Alignments resulted from PCR duplicates or locations in mitochondria were excluded. Only unique alignments within each sample were retained for subsequent analysis. ATAC-seq peaks were called separately for each sample by MACS2 with following options: –keep-dup all –nolambda –nomodel. The ATAC-seq bigwig files were generated using bamcoverage from deeptools. The ATAC-seq signals were visualised in the Integrative Genome Viewer genome browser. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/). For downstream analysis, we normalised the read counts by computing counts scaled by the number of sequenced fragments multiplied by one million (CPM).
Assembly: ARS-UCD1.2
Supplementary files format and content: peaks

Submission date

Dec 14, 2022

Last update date

Jul 20, 2023

Contact name

Zongliang Jiang

E-mail(s)

z.jiang1@ufl.edu

Phone

352-273-8080

Organization name

University of Florida