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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
Organization name Columbia University
Street address 701 West 168th Street
City New York
ZIP/Postal code 10032
Country USA
Platform ID GPL17021
Series (1)
GSE68178 hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function
BioSample SAMN03497962
SRA SRX1004795

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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