|
| Status |
Public on Jun 25, 2021 |
| Title |
C36 F03 WT rep2 Cardiomyocyte |
| Sample type |
SRA |
| |
|
| Source name |
Cardiomyocyte
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Bag3-WT
replicate: rep2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cardiomyocytes and cardiac fibroblasts were isolated from hearts of 16-month Bag3-P209L Tg+ and age matched Bag3-WT mice. Total RNA was extracted from isolated cardiomyocytes and cardiac fibroblasts using an RNEASY kit (Qiagen).
mRNA was enriched using oligo(dT) beads and randomly fragmented by adding fragmentation buffer. cDNA was then synthesized using an (Illumina) RNA library construction kit. Completed libraries, containing unique Illumina adaptors, were then pooled and fed into HiSeq/MiSeq sequencers. Following initial sequencing, cardiomyocyte samples underwent an additional second round of sequencing to increase the total data output.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 4
|
| Data processing |
Kallisto (v0.44.0) count abundance over GENCODE ‘comprehensive gene annotation’ (Release M18) with 50x bootstrap
tximport (v1.6.0) read count input
DESeq2 (v1.18.1) read count normalzation and differential expression analysis
R (v3.4.4) for all other analyses
genome build: GRCm38.p6
processed data files format and content: TSV, raw and normalized counts
|
| |
|
| Submission date |
Jun 25, 2018 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Monte S Willis |
| E-mail(s) |
[email protected]
|
| Phone |
(317) 278-2674
|
| Organization name |
University of Indiana School of Medicine
|
| Street address |
635 Barnhill Street Drive
|
| City |
Indianapolis |
| ZIP/Postal code |
IN 46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN09478952 |
| SRA |
SRX4290494 |
