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| Status |
Public on Nov 21, 2020 |
| Title |
D14_A_ATAC-seq |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Bos taurus |
| Characteristics |
developmental stage/tissue: day 14 elongating embryos
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
not provided; requested
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Feb 10, 2020 |
| Last update date |
Nov 21, 2020 |
| Contact name |
Zongliang Jiang |
| E-mail(s) |
z.jiang1@ufl.edu
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| Organization name |
University of Florida
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| Department |
Animal Sciences
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL24230 |
| Series (1) |
| GSE145040 |
The landscape of accessible chromatin in bovine oocytes and early embryos |
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| Relations |
| BioSample |
SAMN14078863 |
| SRA |
SRX7703300 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4304907_processed_data_file_day14_embryo.peaks.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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