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Sample GSM1905715 Query DataSets for GSM1905715
Status Public on Oct 12, 2015
Title blank36_S6
Sample type SRA
Source name heart, biventricle_blank
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
tissue: heart, biventricle
age: 17 weeks
Extracted molecule total RNA
Extraction protocol Hearts were removed and ventricles were flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent.
Ribosomal RNA depletion along with RNA fragmentation and conversion to paired-end, strand-specific Illumina sequencing libraries were performed with Illumina TruSeq preparation kits for strand-specific, paired-end RNA-Seq.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description rRNA-depleted total RNA
Data processing Illumina Casava1.8 software was used for basecalling. All 76 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 added, and associated bowtie2 index provided by Illumina iGenomes (incorporating the additional mitochondrial RNAs), using tophat v2.0.10 (fr-firststrand)
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 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 Oct 11, 2015
Last update date May 15, 2019
Contact name Scot J Matkovich
Organization name Washington University School of Medicine
Department Center for Cardiovascular Research
Street address 660 S Euclid Ave, box 8086
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platform ID GPL19057
Series (1)
GSE73909 Chronic cardiac contractile dysfunction without hypertrophy does not provoke a compensatory transcriptional response
SRA SRX1327907
BioSample SAMN04160334

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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