|
| Status |
Public on Jan 01, 2024 |
| Title |
LW_Tes_3.RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: testis
breed: Large white
|
| Growth protocol |
All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using TruSeq small RNA sample prep Kits (Illumina, SanDiego, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include TPM values and RPM values for each Sample
|
| |
|
| Submission date |
May 25, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Huo Jinlong |
| E-mail(s) |
jinlonghuo973@gmail.com
|
| Organization name |
Yunnan Agricultural University
|
| Street address |
Jinhei Road 95
|
| City |
Yunnan Kunming |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE233410 |
Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveal regulatory pathways associated with pig testis function |
|
| Relations |
| BioSample |
SAMN35360500 |
| SRA |
SRX20513501 |
