|
| Status |
Public on May 17, 2024 |
| Title |
RU_25_3 |
| Sample type |
SRA |
| |
|
| Source name |
Rumen epithelium
|
| Organism |
Ovis aries |
| Characteristics |
tissue: Rumen epithelium
age: 25 days of age
gender: male
strain: Hu sheep
|
| Growth protocol |
Normal feeding and management on commercial farm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using a total RNA extraction kit (Aidllab, Beijing, China) according to the instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All the RNA samples had integrity greater than 9.
RNA samples were subjected to cDNA library construction using the NEBNext UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
tissue transcriptomic data
|
| Data processing |
Basecalls performed using CASAVA version 1.4.
TopHat2 (v2.0.13) with Bowtie2 (v2.3.3.1) was used to align the high-quality reads to the sheep reference genome (Ovis aries v3.1).
The BAM alignment files that were generated from TopHat2 were sorted by name and converted into SAM files using Samtools (v1.1).
HTSeq-count (v0.9.1) was used to count the number of reads per gene with the SAM files based on the annotation files.
Assembly: Ovis aries v3.1
Supplementary files format and content: Sample was represented by tab-delimited text files including raw counts of each gene for each sample.
|
| |
|
| Submission date |
Apr 06, 2022 |
| Last update date |
May 17, 2024 |
| Contact name |
Bin Yang |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Zhejiang University
|
| Department |
College of Animal Sciences
|
| Lab |
MoE Key Laboratory of Molecular Animal Nutrition
|
| Street address |
No. 866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310013 |
| Country |
China |
| |
|
| Platform ID |
GPL27721 |
| Series (1) |
| GSE200295 |
Transcriptome profiling of multi-chambered stomachs in developing lambs |
|
| Relations |
| BioSample |
SAMN27380672 |
| SRA |
SRX14759443 |
