|
| Status |
Public on Nov 10, 2020 |
| Title |
DOX5 |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: saline control
Sex: male
strain: Wistar
tissue: heart
conditions: 5 weekly iv injections of saline
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with RNeasy® Fibrous Tissue Mini kit (Qiagen, Manchester, UK) using ~30 mg of snap-frozen heart tissue from the saline and DOX high group of cohort 1
Input material was normalised to equal input of 100 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
counts.txt
TIM6297A1
|
| Data processing |
Real time Analysis (RTA): HiSeq 4000 - RTA v2.7.7, Application Version: HD 3.4.0.38
Base-calling: bcl2fastq v2.17.1.14
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.4 with default parameters to the Rat genome Rnor_6.0, Ensembl release 81.
Read counts (abundance measurement): Reads mapping uniquely to genes annotated in ENSEMBL release 81 were counted using featureCounts implemented in subread-v1.5.0
Normalized Counts: Read counts were normalized to counts per million (CPM) and Transcripts per Million (TPM) by dividing each gene-count by total reads mapped (uniquely mapped to exonic regions) per million and using ENSEMBL annotated read-lengths
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: exon_counts.txt: Gene expression counts using reads aligning to annotated exon features of 32546 genes
Supplementary_files_format_and_content: tpm_normalized_counts.txt: The above count table normalized to transcripts per million
Supplementary_files_format_and_content: QC_Table.xlsx: Contains two excel sheets with Sheet 1 = sample information with information regarding sequencing depth and mapping QC metrics
Supplementary_files_format_and_content: QC_Table.xlsx: Sheet2= Contains description of column headers of cell metadata in Sheet 1
Supplementary_files_format_and_content: Text
|
| |
|
| Submission date |
Jul 16, 2020 |
| Last update date |
Nov 10, 2020 |
| Contact name |
Eshita Sharma |
| Organization name |
Wellcome Trust Centre for Human Genetics
|
| Department |
Bioinformatics
|
| Street address |
Roosevelt Drive, Headington
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE154603 |
Targeting mitochondrial metabolism for detection and treatment of doxorubicin-induced heart failure |
|
| Relations |
| BioSample |
SAMN15564107 |
| SRA |
SRX8752558 |
