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Sample GSM1234969 Query DataSets for GSM1234969
Status Public on Feb 15, 2016
Title Heart, Infarcted, rep3
Sample type SRA
 
Source name Heart, Infarcted
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: heart
age: 12 week-old
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Libraries of small RNAs for sequencing were prepared using the DGE-Small RNA Sample Kit, Alternative v1.5 Protocol (Illumina; San Diego, California) according to the protocol supplied with the reagents (Protocol Rev. A, published February 2009) and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx (Illumina) using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents (Catalog FC-104-5020 and GD-300-1001)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Description 12 week old mice, border zone of infarct, 2 weeks after surgery
Data processing Base calling was with Illumina GAP Pipeline Software v1.70
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mouse mature microRNA sequences (from miRBase Version 17) and non-coding RNA sequences (Rfam Version 10) using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as (a/q) x p where a= alignment length, q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches (based on % query) were selected. If a sequence had more than one top match against different database sequences, it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase.
Genome_build: miRBase17
Supplementary_files_format_and_content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format
 
Submission date Sep 19, 2013
Last update date May 15, 2019
Contact name Mark Ibberson
Organization name SIB Swiss Institute of Bioinformatics
Department Vital-IT
Street address Genopode building
City Lausanne
ZIP/Postal code CH-1015
Country Switzerland
 
Platform ID GPL9250
Series (2)
GSE51014 Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways
GSE51019 Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways
Relations
BioSample SAMN02359207
SRA SRX355607

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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