 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2024 |
| Title |
ATAC_Sus_MII_GCs_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: ovary
cell type: granulosa cells
treatment: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In brief, a total of 50 oocytes with zona pellucida removed, and 50,000 GCs were lysed respectively in lysis buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3mM MgCl2, 0.1%Igepal CA-630, 0.1%Tween-20, 0.01%Digitonin, 1% Cytochalasin B, 0.1%collagenase I) for 10 min on ice to generate the nuclei. Nuclei were then spun at 500g for 5 min immediately to remove the supernatant. Tn5 transposome and tagmentation procedures were subjected at 37°C for 30 min (Vazyme, TD501).
DNA were purified using 2×AMPure beads (Beckman, A63881) and conducted to 16 cycles (for oocytes) or 14 cycles (for GCs) of library amplification using the following PCR conditions: 72°C for 3 min; 98°C for 30s; and thermocycling at 98 °C for 15s, 60°C for 30 s and 72°C for 3 min; following by 72°C 5 min.The amplified DNA was size-selected using AMPure beads for 200–500bp DNA fragments. All libraries were sequenced by the Novaseq 6000 platform to at least a depth of 4.0×107 reads accordingly.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FastQC was used to evaluate the quality of the sequencing data, and Trimmomatic was explored to remove the adaptor sequences and obtain the clean data, which were subsequently aligned to the UCSC mm10 or Sscrofa11.1 reference genome using Bowtie2, under the parameters -t -q -N 1 -L 25.
All unmapped reads, non-uniquely mapped reads, and PCR duplicates were removed. For downstream analysis, the MACS2 was applied to call significant peaks with q-value < 0.05. To identify differentially expressed genes between different passaged GCs, the ATAC-seq peaks of each sample were merged to generate a consensus set of unique peaks.
The number of peaks among this set was counted using bedtools, and GAAs and GIAs were identified using DESeq2, with thresholds log2(fold-change) ≥ 1 and p value < 0.05.
Genomic features of peaks were annotated using ChIPseeker R package. Additionally, to find the sequence motifs enriched in distal ATACseq peaks, findMotifsGenome.pl from the HOMER program was used.
Motifs with known match in HOMER database were selected in GAAs and GIAs. Promoters were defined as ±2.5 kb around the TSS. Peaks at least 2.5 kb away from TSSs were defined as distal peaks by BEDTools.
The DAVID web-tool was employed to identify the GO terms using databases including Molecular Functions, Biological Functions and Cellular Components.
Genome-wide normalized signal coverage tracks were created by bam Coverage in deepTools and were visualized in the Integrative Genomics Viewer.
Assembly: Sscrofa11.1 and mm10
Supplementary files format and content: bigWig files include peaks for each sample, respectively.
|
| |
|
| Submission date |
May 20, 2024 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Yiting Guan |
| E-mail(s) |
yt_guan@yeah.net
|
| Organization name |
Guangdong Medical University
|
| Department |
Zhanjiang Institute of Clinical Medicine
|
| Street address |
236 Yuanzhu Road
|
| City |
Zhanjiang |
| ZIP/Postal code |
524045 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (2) |
| GSE267850 |
Fosl2 orchestrates chromatin accessibility to determine granulosa cells developmental events in mammals [ATAC-seq] |
| GSE267974 |
Fosl2 orchestrates chromatin accessibility to determine granulosa cells developmental events in mammals |
|
| Relations |
| BioSample |
SAMN41455463 |
| SRA |
SRX24605969 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8279840_ATAC_Sus_MII_GCs_Rep1.bw |
193.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
