|
Status |
Public on Dec 26, 2022 |
Title |
NC_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 normal saline time point: Day 13 individual: NC_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.
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|
|
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 |
SAMN32348894 |
SRA |
SRX18805151 |