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Sample GSM2059620 Query DataSets for GSM2059620
Status Public on Apr 13, 2017
Title HLHS_635-260-1-LV
Sample type SRA
 
Source name left ventricle, HLHS, E13.5
Organism Mus musculus
Characteristics strain/background: C57BL/6
phenotype: hypoplastic left heart syndrome (HLHS)
developmental stage: E13.5
tissue: heart ventricle
side: left
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from mouse embryonic hearts using the miRNeasy micro Kit (QIAGEN) with on-column DNase I digestion method (QIAGEN).
Libraries were constructed using TruSeq RNA Sample Preparation Lit v2 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description HLHS_260-1-LV
Processed data file: counts.txt
Processed data file: deResults.xlsx
Data processing Reads were aligned using TopHat2 (v2.0.9) with the following options: --segment-length 25 --segment-mismatches 2 --no-novel-juncs --min-achor=8 --splice-mismatches 0 --max-intron-length 500000 --microexon-search --no-mixed --no-coverage-search and values for the inner mate distance estimated using RSeQC (v2.3.6).
PCR duplicates were removed using the MarkDuplicates utility from the Picard suite of tools (v1.96).
Gene-level counts were calculated by HTSeq-count (v0.5.4p5) using "union" mode and Ensembl GTF file as retrieved from iGenomes (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/README.txt; Ensembl release 66) for mm9.
Differential expression analyses were performed using the R package edgeR (v3.4.2). Genes with low expression (counts-per-million < 1 in all samples) were discarded. Dispersion parameters were estimated accounting for side (LV and RV), stage (E13.5, E14.5, and E17.5), disease (HLHS and control), and their pairwise interactions. For each gene, the maximum of common, trended and tag-wise dispersion estimate was used for subsequent analyses. Linear contrasts were used to compare HLHS to control in LV and RV, respectively, using likelihood ratio tests. Genes with an FDR <=0.05 and a fold-change >= 1.5 were considered significantly differentially expressed.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file with raw gene-level counts for all samples.
Supplementary_files_format_and_content: deResults.xlsx: Excel spreadsheets for results of the differential expression analyses in LV (HLHS vs. Control) and RV (HLHS vs. Control), respectively. These additionally include the counts-per-million (cpm) values (log2 with pseudocount 1) for all analyzed genes.
 
Submission date Feb 10, 2016
Last update date May 15, 2019
Contact name Cecilia W Lo
E-mail(s) cel36@pitt.edu
Organization name University of Pittsburgh
Department Developmental Biology
Street address 530 45th St., 8120 Rangos Research Center
City Pittsburgh
State/province PA
ZIP/Postal code 15201
Country USA
 
Platform ID GPL13112
Series (2)
GSE77798 Pathogenesis of Hypoplastic Left Heart Syndrome [RNA-seq]
GSE77799 The complex genetics of hypoplastic left heart syndrome
Relations
SRA SRX1570954
BioSample SAMN04501081

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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