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Sample GSM1686490 Query DataSets for GSM1686490
Status Public on Dec 04, 2015
Title P21_ntg_10547-1
Sample type SRA
 
Source name P21_ntg_heart_left ventricle
Organism Mus musculus
Characteristics strain background: FVB/N
genotype/variation: nontransgenic (ntg)
age: P21 (3 weeks)
tissue: heart, left ventricle
Extracted molecule polyA RNA
Extraction protocol Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per Methods Mol Biol. 2015;1299:27-49, PMID 25836573.
non-strand-specific, single-end RNA-Seq
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.6 and Casava1.8 software was used for basecalling. All 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the transcriptome, defined by annotation based on the UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs and human-Mfn2 cDNA), using tophat v2.0.10.
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the supplied gtf, based on UCSC mm10 genes.gtf but with mitochondrial RNAs and human-Mfn2 cDNA added.
htseq-count data allows each user maximum flexibility in performing sample (library) depth normalization and differential gene expression using software such as DESeq or edgeR.
Additionally, we used Cufflinks v2.1 to calculate FPKM for each gene entry in each library. However, this was merely done for later graph display. Actual calculations of differential gene expression used htseq-count data as input to DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: single tab-delimited text files include htseq-count values for each gene, or FPKM values for each gene.
 
Submission date May 15, 2015
Last update date May 15, 2019
Contact name Scot J Matkovich
E-mail(s) sjmatkovich@lilly.com
Organization name Eli Lilly and Company
Street address Lilly Corporate Center
City Indianapolis
State/province IN
ZIP/Postal code 46285
Country USA
 
Platform ID GPL17021
Series (1)
GSE68921 Parkin-mediated mitophagy evokes perinatal cardiac mitochondria maturation
Relations
BioSample SAMN03658613
SRA SRX1029355

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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