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Sample GSM1029437

Query DataSets for GSM1029437

Status

Public on Nov 20, 2014

Title

22 dpp

Sample type

SRA

Source name

22 dpp testis

Organism

Mus musculus

Characteristics

strain: C57BL6/J
age: 22 dpp
tissue: testis
genetic background: C57BL/6

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Trizol reagent from testes or FACS-purified cells.
Libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Directional

Data processing

Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)).
Genome_build: mm9
Supplementary_files_format_and_content: [Gene ID] [Gene name] [6dpp RPKM] [10dpp RPKM] [15dpp RPKM] [18dpp RPKM] [22dpp RPKM] [28dpp RPKM] [40dpp RPKM]

Submission date

Nov 01, 2012

Last update date

May 15, 2019

Contact name

Toshiaki Watanabe

E-mail(s)

toshwatatoshiakiwatanabe@gmail.com

Phone

81-55-981-6796

Organization name

Yale University