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Sample GSM2982708

Query DataSets for GSM2982708

Status

Public on Jul 22, 2019

Title

Remote zone-3.1

Sample type

SRA

Source name

Remote zone left ventricular tissue post myocardial infarction

Organism

Mus musculus

Characteristics

strain: FVB/N
stress: myocardial infarction
tissue: remote zone left ventricular tissue post myocardial infarction
time: 3 days post-stress
sample type: animal-3.1

Treatment protocol

Tamoxifen (20 mg/kg) was administrated i.p. one week prior to t=0 and repeated the two following days. Myocardial infarction was performed as described previously in Sergeeva et al., 2013.

Growth protocol

Animal care and experiments conform to the Directive 2010/63/EU of the European Parliament. All animal work was approved by the Animal Experimental Committee of the Academic Medical Center, Amsterdam, and was carried out in compliance with the Dutch government guidelines. Myh6-MerCreMer (Sohal et al., 2001) , nTnG (JAX stock #023035) and Gt(ROSA)26Sortm5(CAG-Sun1/sfGFP)Nat/J (JAX stock #021039) mice were bred on the FVB/N background.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen).
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads
Total RNA was extracted from the border zone, remote zone, and the LV of sham-operated mice at 3, 7, and 14 dpi using RNAzol according to manufacturer’s instructions (Sigma-Aldrich). Prior to cDNA synthesis, total RNA samples were treated with RNase-free DNase I according to manufacturer’s instructions (Invitrogen). The cDNA synthesis was carried out on 500 ng DNase-treated RNA using oligo-dT following the Superscript II system protocol (Invitrogen). For ATAC-seq, isolated nuclei were GFP sorted on a SH800 flow cytometer (Sony). Samples were gated in such a way that debris, nuclei clumps, and nuclei with no cardiomyocyte origin were excluded. A total of 50.000 nuclei per sample was collected and successively washed with PBS and used as input for ATAC-seq. Prior to sequencing, a quality check was performed to assure cardiomyocyte-specific open chromatin
For RNA-seq libraries, 40 ng DNase-treated total RNA was amplified and converted to cDNA using the Ovation RNA-seq v2 kit (NuGEN). Amplified cDNA was sheared to an average fragment length of 200-400 bp and used with the SOLiD system (Life Technologies) to generate index-tagged sequencing libraries. Library quality and size distribution were determined with TapeStation (Agilent Technologies). Pooled libraries sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

RNA-MI-counts.xlsx
RM-3.1

Data processing

Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al., 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014).
Genome_build: mm10 (RNA-seq)
Supplementary_files_format_and_content: RNA-seq: MI-counts.xlsx (Excel file with raw and normalized (DESeq2) count data per gene & differential expression analysis).

Submission date

Feb 06, 2018

Last update date

Jul 22, 2019

Contact name

Vincent M. Christoffels

E-mail(s)

v.m.christoffels@amsterdamumc.nl

Phone

0205667821

Organization name

Amsterdam UMC