|
| Status |
Public on Dec 26, 2022 |
| Title |
SA_2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
rumen epithelial tissue
|
| Organism |
Capra hircus |
| Characteristics |
breed: Guanzhong
disease state: healthy
tissue: rumen epithelial tissue
treatment: infusion of sodium acetate
time point: Day 13
individual: SA_2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for rumen epithelial transcriptome sequencing was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to ARS1.2 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: ARS1.2
Supplementary files format and content: Rumen_gene_count_matrix.csv: Comma-delimited text file includes gene counts for each Sample.
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
Dec 26, 2022 |
| Contact name |
Yongkang Zhen |
| E-mail(s) |
dx120220164@stu.yzu.edu.cn
|
| Phone |
15062800765
|
| Organization name |
Yangzhou University
|
| Street address |
Yangzhou University
|
| City |
Yangzhou |
| State/province |
— Please Select — |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL32967 |
| Series (2) |
| GSE221507 |
RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids [RNA-seq] |
| GSE221509 |
RNA-Seq data of ruminal epithelial tissue and 16S rRNA sequencing data of rumen digesta in goats infusion of three short-chain fatty acids |
|
| Relations |
| BioSample |
SAMN32348891 |
| SRA |
SRX18805154 |
