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Sample GSM1665134

Query DataSets for GSM1665134

Status

Public on May 26, 2015

Title

Hnrnpu mutant rep2

Sample type

SRA

Source name

Heart, Hnrnpu mutant

Organism

Mus musculus

Characteristics

strain/background: C57BL/6 & 129 S4 mix
genotype/variation: hnrnpu mutant
tissue: ventricle
age: postnatal day 14
gender: female

Treatment protocol

N/A

Growth protocol

N/A

Extracted molecule

total RNA

Extraction protocol

Whole hearts were dissected from P14 mice of distinct genotypes, atria were removed. Total RNAs were extracted from ventricles by Trizol extraction protocol.
Libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

MT_2

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and then mapped to the mm9 whole genome using Bowtie v0.12.9 with parameters -X 20000 -k 2 -m 2 -q -p
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. Differential gene expression was calculated using the R statistical package DESeq.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: hnrnpu-heart-P14.xlsx: Tab-delimited text file includes RPKM values for each Sample.

Submission date

Apr 22, 2015

Last update date

May 15, 2019

Contact name

Sean O'Keeffe

E-mail(s)

so2346@columbia.edu

Organization name

Columbia University

Street address

701 West 168th Street