|
| Status |
Public on Jul 22, 2019 |
| Title |
Remote Myocardium mouse 43 [RM-43] |
| Sample type |
SRA |
| |
|
| Source name |
Cardiomyocytes remote myocardium
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
age: 8 weeks
time point: 7 days after LAD
tissue: infarcted myocardium
tissue subtype: Cardiomyocytes remote myocardium
molecule subtype: nuclear RNA
|
| Treatment protocol |
Border zone and remote myocardium were microdissected and snap-frozen
|
| Growth protocol |
Murine cardiac tissue was obtained 7 days after LAD (Ligation of the left ascecning permanent ligation of the left anterior descending coronary artery)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were extracted from snap-frozen samples, and stained with PCM-1 rabbit polyclonal antibody (Atlas Antibodies) for flow cytoemtry analysis. RNA was isolated using the RNeasy Plus MicroKit (Quiagen)
NuGEN's Ovation RNA-seq V2 kit. Input cDNA synthesis: 500 pg
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
PCM-1 sorted
|
| 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, Huber, and Anders 2014).
Genome_build: mm10
Supplementary_files_format_and_content: BZ-PCM1-RNA-seq-counts.xlsx (Excel file with normalized (DESeq2) count data per gene & differential expression analysis).
|
| |
|
| Submission date |
Mar 08, 2019 |
| Last update date |
Sep 01, 2021 |
| 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 |
GPL21103 |
| Series (1) |
| GSE128034 |
Transcriptional characterization of the myocardial infarct border zone |
|
| Relations |
| Reanalyzed by |
GSM5552403 |
| BioSample |
SAMN11087708 |
| SRA |
SRX5494738 |
