|
| Status |
Public on Jan 28, 2022 |
| Title |
4W-1 mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Goat kid
|
| Organism |
Capra hircus |
| Characteristics |
age: 4 weeks of age
tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver tissue were quickly collected after slaughter, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeqTM stranded total RNA Kit(San Diego, CA) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4W-1
Goat kid
|
| Data processing |
Paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq6000 (2 × 150bp read length)
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Clean reads were separately aligned to the goat (Capra_hircus) reference genome (ARS1) with orientation mode using HIASAT (https://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
The expression level of each transcript was calculated according to fragments per kilobases per million reads (FPKM) method.
Genome_build: ARS1
Supplementary_files_format_and_content: Tab-delimited text files include gene FPKM values for each Sample
|
| |
|
| Submission date |
Jan 21, 2022 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Chao Tianle |
| E-mail(s) |
chaotianle@sdau.edu.cn
|
| Phone |
15153876133
|
| Organization name |
6/5000 Shandong Agricultural University
|
| Street address |
Daizong street, no. 61, 6/5000 Shandong Agricultural University
|
| City |
Tai’an |
| State/province |
Shandong |
| ZIP/Postal code |
538 |
| Country |
China |
| |
|
| Platform ID |
GPL27106 |
| Series (1) |
| GSE194190 |
mRNA expression profile in the Laiwu black goat kid liver |
|
| Relations |
| BioSample |
SAMN25161682 |
| SRA |
SRX13860862 |
