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Sample GSM2236108 Query DataSets for GSM2236108
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 Utrecht University
Department Biology
Lab Reproductive Biology
Street address Padualaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584CH
Country Netherlands
 
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

Supplementary file Size Download File type/resource
GSM2236108_Trilostane_1.txt.gz 130.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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