|
| Status |
Public on Jun 14, 2018 |
| Title |
GP_BF_12_KID |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Cavia porcellus |
| Characteristics |
strain: HsdDhl:DH
Sex: female
tissue: kidney
age: 0.96 years
reproductive status: breeder
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extraction was done as described in Bens et al. 2016. (PMID:26763976)
Library preparation was done using Illumina's TruSeq RNA Library Prep Kit v2 kit following the manufacturer's description.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Extraction of read information in FastQ format was done using the tool bcl2astq v1.8.4 (provided by Illumina).
Reads were mapped using STAR (v2.4.1d) with a maximum mismatch of 6% and a minimum aligned length of 90%. Reads mapped to multiple loci were discarded.
Reads per gene were counted using HTSeq framework (0.6.1p1)
Genome_build: genome (cavpor3) can be download from UCSC (ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/)
Supplementary_files_format_and_content: The Excel sheet includes raw counts for all genes and each sample.
|
| |
|
| Submission date |
May 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Marco Groth |
| E-mail(s) |
dnaseq@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22346 |
| Series (2) |
| GSE98653 |
RNA-seq of ten guinea pig tissues from breeders and non-breeders |
| GSE98719 |
RNA-seq of breeding and non-breeding naked mole-rats and guinea pigs |
|
| Relations |
| BioSample |
SAMN06915580 |
| SRA |
SRX2789519 |
