|
| Status |
Public on Nov 02, 2023 |
| Title |
4D |
| Sample type |
SRA |
| |
|
| Source name |
HEART
|
| Organism |
Mus musculus |
| Characteristics |
tissue: HEART
strain: C57BL6
gender: male
treatment: 4 DAY ISOPROTERNOL
|
| Treatment protocol |
C57BL6 male mice were administered with subcutaneous Isoproterenol for 4,8 and 11 days and saline as controls.
|
| Growth protocol |
Animals were maintained in individually ventilated cages with ad libitum access to chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZOL. DNA was depleted using DNaseI.
RNA libraries for RNA-seq were prepared using Illumina TrueSeq total RNA kit following manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v4.1 (quality cutoff:20 and min read length cutoff:50)
Trimmed sequence reads were mapped to GRCm38.p6 using HISAT2 v2.2.1
Gene and Isoform abundances were quantified using RSEM v1.3.3
Normalisation and RNA-seq differential expression was done in DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files includes gene counts, TPM and FPKM for each sample
Supplementary files format and content: Tab-delimited text files includes isoform counts, TPM and FPKM for each sample
|
| |
|
| Submission date |
Jul 31, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Kumarswamy Regalla |
| E-mail(s) |
rk@ccmb.res.in
|
| Organization name |
CCMB
|
| Street address |
Centre for Cellular and Molecular Biology (CSIR-CCMB), Habsiguda
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500007 |
| Country |
India |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE239653 |
Transcriptional changes during Isoproterenol induced cardiac fibrosis in mice |
|
| Relations |
| BioSample |
SAMN36772701 |
| SRA |
SRX21200063 |
