|
| Status |
Public on Apr 15, 2024 |
| Title |
R7_Sham-H_f_LV_#154_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
left ventricle
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain background: F1-generation children derived from female Wistar Kyoto x male Lewis rat
cell type: cardiac myocytes
tissue: left ventricle
Sex: female
animal id: 154
age: 11 weeks
treatment: sham
disease progression: compensatory
treatment time: 7 weeks
|
| Treatment protocol |
6 month old weanling rats were clipped nonconstrictively at the pulmonary artery or aorta respectively. Compensatory hypertrophy of left or right ventricle developed 7 weeks after banding, after which the samples for the compensatory phase were harvested. Heart failure developed 22 (right ventricle) or 26 (left ventricle) weeks, after which decompensatory samples were harvested
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After extraction and perfusion for cleanup, fre hearts were digested using collagenase II in a Langendorff aparatus for 25 minutes. Afterwards the ventricles were seperated, cut into small pieces and digested again with collagenase II for 5min. Afterwards the suspension was filtered using a nylon filter (200µm), and cardiac myocytes seperated from other cell types via a series of centrifugation steps.
RNA was extracted using Macherey & Nagel Nucleospin RNA kit
Libraries were prepared by Novagene using a rRNA depletion strategy
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
col_names:"raw.reads.sham_compensatory_female_#154_LV", "normalized.reads.sham_compensatory_female_#154_LV", "fpkm.sham_compensatory_female_#154_LV"
cardiac_myocytes_reads.csv
cardiac_myocytes_DEseq2_Output.xlsx
|
| Data processing |
Nexflow nf/core rna_seq v3.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimgalore integrated into nf-core/rnaseq (parameter- Quality limit: 20)
Trimmed reads were mapped to rnor6 usinf STAR integrated into nf-core/rnaseq (default parameters)
Readcount extraction was perfomed using FeatureCounts (Rsubreads v2.2.6), disallowing multiple overlap
Normalization and differential expression analysis was performed using DEseq2 1.28.1, using the independed filtering option and beta_prior LFC-shrinkage
Assembly: rnor6
Supplementary files format and content: bigwig files
Supplementary files format and content: unnormalized read count, DEseq2-normalized read count and FPKM count tables in single csv-file
Supplementary files format and content: DEseq2 Output in Excel file
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Axel Weber |
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Rudolf Buchheim Institute of Pharmakology
|
| Street address |
Schubertstrasse 81
|
| City |
Giessen |
| State/province |
Hesse |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE216263 |
Transcriptome changes in cardiomyocytes isolated from a rat model of progressive heart failure |
|
| Relations |
| BioSample |
SAMN31398855 |
| SRA |
SRX17981788 |
