|
| Status |
Public on Sep 13, 2016 |
| Title |
Trilostane_1 |
| Sample type |
SRA |
| |
|
| Source name |
Testis
|
| Organism |
Danio rerio |
| Characteristics |
tissue: testis
age: Adult
genotype: Wild type
incubation: 48 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from testis tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio-analyzer 2100 total RNA Nano series II chip (Agilent)
Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Image analysis and base calling were done by the Illumina pipeline (CASAVA software v1.8)
The read counts were extracted using the Python package HTSeq, and normalized using the totally mapped reads per library
Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome (Zv9) using STAR v2.3 (standard parameters for single-end reads)
Differential expression analysis was performed using the R/Bioconductor package NOISeq
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and raw counts for each sample.
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Diego Crespo |
| E-mail(s) |
diegocrespomorao@gmail.com
|
| Organization name |
Institute of Marine Research
|
| Department |
Reproduction and Developmental Biology
|
| Street address |
Nordnesgaten 50
|
| City |
Bergen |
| ZIP/Postal code |
5005 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE84436 |
Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis |
|
| Relations |
| BioSample |
SAMN05392207 |
| SRA |
SRX1950207 |
