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Sample GSM1229972

Query DataSets for GSM1229972

Status

Public on Sep 29, 2013

Title

WT-mRNA-seq-testis

Sample type

SRA

Source name

WT testis expression mRNA-seq

Organism

Mus musculus

Characteristics

tissue: testis
age: 3-month old
genotype/variation: wild type

Extracted molecule

polyA RNA

Extraction protocol

Total RNAs were extracted individually from 3-month-old WT and Taf7l-/Y mice testis (6 of each group) by RNeasy Plus Mini Kit (Qiagen Inc., Germantown, MD).
mRNA-seq libraries preparation and deep sequencing: 6 extracted RNAs from WT and KO testes were pooled with equal amount and 8 μg of WT and KO pooled RNA samples was used to purify mRNA and subsequently converted into to mRNA-seq library using mRNA-Seq Sample Prep Kit (Illumina Inc., San Diego, CA) and sequenced on an Illumina HiSeq 2000 sequencer.qualities of the libraries were assessed by 2100 Bioanalyzer (Functional Genomics Laboratory, Berkeley,CA) and then subjected to ultra-high throughput sequencing on an Illumina HiSeq 2000 sequencer (GSL core facility, UC Berkeley, CA) as previously described (Zhou et al., 2013), each sample yielded ∼100–200 million reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Mapping sequencing reads to the genome: Sequenced reads were mapped to the July 2007 assembly of the mouse genome (UCSC version mm9, NCBI37) using Bowtie (Langmead et al., 2009) with the command-line options ‘-c -q -n 2 -l 48 -m 1’, thereby keeping for further analyses only reads that mapped uniquely to the genome with at most two mismatches at the first 48 bases.
Digital gene expression of mRNA-seq: The reads were then mapped to the mouse transcriptome (created using UCSC table browser, version mm9, on February 2012), using TopHat (Trapnell et al., 2009), version v1.4.0., using default parameters. We then applied cufflinks (Trapnell et al., 2010), version v1.3.0, using the default parameters except: --max-mle-iterations 1, to estimate the digital expression levels at each transcript.
Genome_build: MGSCv37 (mm9)

Submission date

Sep 12, 2013

Last update date

May 15, 2019

Contact name

Haiying Zhou

E-mail(s)

zhouh@berkeley.edu

Organization name

HHMI/UCB

Department

MCB