|
| Status |
Public on Jul 29, 2021 |
| Title |
Duroc rep3_mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Duroc_mRNA
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Longissimus dorsi muscle
strain: Duroc
Sex: male
age: post natal day 180
|
| Growth protocol |
180-day-old male pigs were fed under the same feeding conditions for 180 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ATAC-seq: The original Illumina high-throughput sequencing image data files were converted into original sequences after base group recognition by bcl2fastq software. The results were stored in FASTQ file format. Trimmomatic (v0.36) software was used to filter the original sequences to obtain high quality clean reads, and Bowtie2 software was used to compare the sequencing sequences with the reference genome (Sus scrofa 11.1). RNA-seq: Transcriptome data were assembled using Stringtie and compared with the reference genome (Sus scrofa 10.2) using CuffCompare.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
180-day-old male pigs were fed under the same feeding conditions for 180 days
mRNA_FPKM&log2Ratio
|
| Data processing |
ATAC-seq: MACS2 software was used for peak detection to obtain an overview of the open chromatin regions of the whole genome of each sample.
RNA-seq: We used Bowtie2 to align clean reads to the reference sequence, and then we used RSEM to calculate the gene and transcriptome expression.
Genome_build: Genome_build: Sus scrofa 11.1 (ATAC-seq)& Sus scrofa 10.2 (RNA-seq)
Supplementary_files_format_and_content: ATAC-seq: Luchuan peaks& Duroc peaks& Common peaks
Supplementary_files_format_and_content: RNA-seq: FPKM& log2Ratio
|
| |
|
| Submission date |
Jul 26, 2021 |
| Last update date |
Jul 29, 2021 |
| Contact name |
Lei Zhou |
| E-mail(s) |
jk19900812@126.com
|
| Organization name |
Guangxi university
|
| Department |
College of Animal Science and Technology
|
| Street address |
Daxuedong Road, Xixiangtang District
|
| City |
Nanning |
| State/province |
Guangxi |
| ZIP/Postal code |
530004 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE180840 |
Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs |
|
| Relations |
| BioSample |
SAMN20407839 |
| SRA |
SRX11555367 |
