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Sample GSM4304906

Query DataSets for GSM4304906

Status

Public on Nov 21, 2020

Title

Vivo_BL_4_ATAC-seq

Sample type

SRA

Source name

embryos

Organism

Bos taurus

Characteristics

developmental stage/tissue: Blastocyst derived in vivo

Extracted molecule

genomic DNA

Extraction protocol

not provided; requested

Library strategy

ATAC-seq

Library source

genomic

Library selection

other

Instrument model

HiSeq X Ten

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 locating in mitochondria were excluded. Only unique alignments within each sample were retained in subsequent analysis. Principle component analysis (PCA) was performed on pairwise correlation data in R with functions prcomp. ATAC-seq peaks were called separately for each sample by MACS2 with following options: --keep-dup all –nolambda --nomodel. Peaks in individual samples from the same development stage were subsequently merged using bedtools (https://bedtools.readthedocs.io/en/latest/).
For downstream analysis, we normalized the read counts by computing the number of reads per kilobase of bin per million of reads (RPKM). To visualize the ATAC-seq signal in the UCSC genome browser, we extended each read by 250bp and counted the coverage for each base. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/).
Genome_build: UMD3.1.1
Supplementary_files_format_and_content: peaks

Submission date

Feb 10, 2020

Last update date

Nov 21, 2020

Contact name

Zongliang Jiang

E-mail(s)

z.jiang1@ufl.edu

Organization name

University of Florida

Department

Animal Sciences