|
| Status |
Public on Jul 05, 2016 |
| Title |
LA-kidney |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Sus scrofa |
| Characteristics |
age: 60 days old
tissue: kidney
breed name: Landrace
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted using the TrIzol reagent (Life Technologies, Beijing, China) according to the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit was used with 1 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 HiSeq 2500 |
| |
|
| Description |
LA_exp.txt
|
| Data processing |
Illumina Casava1.82 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to itself assembly genome using Tophat.
Cufflinks version 2.2.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mingzhou Li |
| E-mail(s) |
mingzhou.li@163.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
No.211 Huimin Road, Wenjiang District
|
| City |
chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL19176 |
| Series (1) |
| GSE77776 |
Transcriptome data used for gene annotation |
|
| Relations |
| BioSample |
SAMN04484981 |
| SRA |
SRX1569859 |
