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Sample GSM1380723 Query DataSets for GSM1380723
Status Public on Jan 01, 2015
Title P00333 Idiopathic Dilated CMP Left Ventricle
Sample type SRA
Source name heart left ventricle, idiopathic dilated CMP
Organism Homo sapiens
Characteristics tissue: heart left ventricle
heart failure: yes
disease status: idiopathic dilated CMP
gender: female
age: 59
ethnicity: White/Caucasian
Treatment protocol Explanted myocardium snap frozen in liquid nitrogen.
Growth protocol None
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Illumina TruSeq® RNA Sample Preparation v2 with the final product size selected between 350 and 650 bp.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
Description P00333
PolyA mRNA
Data processing Illumina Casava1.8 software used for basecalling.
The RNA-seq data were aligned to the hg19 reference genome using Tophat with default options.
Transcripts were assembled using Cufflinks. For differentially expressed genes, we carried out functional annotation analysis using DAVID; we further examined whether they were more likely to overlap with GWAS findings, the analysis was based on all GWAS signals summarized in the NHGRI GWAS catalogue.
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM_TRACKING file: Expression values as FPKMs were calculated using Cufflinks and RefSeq gene annotations. Columns are Official gene symbol, hg19 gene locus, FPKM expression value.
Supplementary_files_format_and_content: cuffdiff .txt file: Differential expression results from the cuffdiff program. Columns are Gene Symbol, gene locus, FPKM of group 1, FPKM of group 2 and an adjusted P value.
Submission date May 06, 2014
Last update date May 15, 2019
Contact name Michael Patrick Morley
Phone 215-898-2026
Organization name Perelman School of Medicine at the University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL9052
Series (2)
GSE57344 RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [RNA-seq]
GSE57345 RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure
BioSample SAMN02746606
SRA SRX533785

Supplementary file Size Download File type/resource
GSM1380723_P00333_DCM.fpkm_tracking.gz 364.6 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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