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Sample GSM1559541

Query DataSets for GSM1559541

Status

Public on Jul 20, 2015

Title

3'-Seq mouse Brain Rep2

Sample type

SRA

Source name

brain

Organism

Mus musculus

Characteristics

strain: C57BL/6
gender: male
age: 8 weeks
tissue: brain

Extracted molecule

total RNA

Extraction protocol

Sample preparations for 3′-seq was performed as previously reported (Lianoglou et al., Genes & Development, 2013) using total RNA extracted from 8 week-old C57BL/6 male mouse tissue, including testis, liver, brain, and skeletal muscle.
3'-seq libraries were prepared for sequencing using previously reported protocol(Lianoglou et al., Genes & Development, 2013).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 1500

Description

Protocol: 3'-seq

Data processing

Illumina RTA 1.17 software used for basecalling.
Sequenced reads were mapped to the mouse genome (mm9) with STAR alignment software (Dobin et al., 2013) and the parameter “--outFilterMultimapNmax 1 --alignIntronMax 1” (no multi-hit reads, no splice prediction) to treat poly-A containing reads.
Quantification of each gene was performed by counting the number of reads that were mapped around the 3′-UTR region and then normalizing the number as reads per million (RPM) per region. In the case of novel histone H3 variant genes, the region within 3 kb from the end of a coding sequence was defined as the putative 3'-UTR.
genome build: mm9
processed data files format and content: tab-delimited text files include RPKM values for each Sample
processed data file: 3primeSeq_RPMTable_rep2.txt.gz

Submission date

Dec 05, 2014

Last update date

May 15, 2019

Contact name

Yasuyuki Ohkawa

E-mail(s)

yohkawa@bioreg.kyushu-u.ac.jp

Organization name

Kyushu University

Department

Medical Institute of Bioregulation, Medical Institute of Bioregulation