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Sample GSM5548040

Query DataSets for GSM5548040

Status

Public on Jan 20, 2022

Title

DRy2 (Young, Rep 2)

Sample type

SRA

Source name

Heart ventricle

Organism

Danio rerio

Characteristics

tissue: ventricle
age: 7 months

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from zebrafish ventricles using Trizol.
Preparation of libraries was done using NEBNext Ultra II directional RNA library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according the manufacturer‘s description.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422
Reads were aligned to the Zebrafish reference genome (GRCz11 with the Ensembl genome annotation Release 95) using STAR 2.5.4b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.6.3 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Genome_build: GRCz11
Supplementary_files_format_and_content: csv file containing read counts per gene over all samples

Submission date

Aug 28, 2021

Last update date

Jan 20, 2022

Contact name

Philipp Koch

Organization name

Leibniz Institute on Aging - Fritz Lipmann Institute

Department

Core Facility Life Science Computing

Street address

Beutenbergstraße 11