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Sample GSM5237146 Query DataSets for GSM5237146
Status Public on Oct 13, 2021
Title Testis3
Sample type SRA
 
Source name zebrafish testis
Organism Danio rerio
Characteristics genotype: wild-type
tissue: testis
strain: TLAB
Growth protocol Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle)
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using the standard TRIzol (Invitrogen) protocol. To obtain polyA+ RNA, the poly(A) selection kit from LEXOGEN was used.
Strand-specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode
BAM files containing sequencing reads were converted to fastq files using samtools (v1.9)
Barcoded libraries were demultiplexed using fastx-toolkit (v0.0.14)
Sequencing adapters were trimmed with cutadapt (v1.18) and only reads longer than 25 bases were kept
Reads were aligned to GRCz11 with Hisat2 v2.1.0, using the Ensembl transcriptome release 102. The following parameters were used: hisat2 -q --dta --rna-strandness R -k 12 --no-unal
Quantification at the gene level (to obtain transcript per million (TPM)) was perfomed using Kallisto (v0.43.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab delimited files containing TPM
 
Submission date Apr 12, 2021
Last update date Oct 13, 2021
Contact name Luis Enrique Cabrera Quio
E-mail(s) luis.cabrera.quio@imp.ac.at
Organization name Research Institute of Molecular Pathology
Lab Pauli lab
Street address Campus Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL18413
Series (1)
GSE171906 RNA-Seq from zebrafish adult tissues
Relations
BioSample SAMN18715719
SRA SRX10579922

Supplementary file Size Download File type/resource
GSM5237146_Gene_abundance_Testis3.tsv.gz 514.9 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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