|
| Status |
Public on Jul 22, 2019 |
| Title |
Border zone-7.9 |
| Sample type |
SRA |
| |
|
| Source name |
Border zone left ventricular tissue post myocardial infarction
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
stress: myocardial infarction
tissue: border zone left ventricular tissue post myocardial infarction
time: 7 days post-stress
sample type: animal-7.9
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-MI-counts.xlsx
BZ-7.9
|
| 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
|
| Department |
Medical Biology
|
| Lab |
Vincent Christoffels
|
| Street address |
Meibergdreef 15 K2-159
|
| City |
Amsterdam |
| State/province |
N/A (NA) |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE110209 |
Spatiotemporal pattern of the transcriptional regulatory landscape of the mouse ventricle after myocardial infarction |
|
| Relations |
| BioSample |
SAMN08471549 |
| SRA |
SRX3653339 |
