|
| Status |
Public on Jul 31, 2018 |
| Title |
IRT3-II [TH6_t2] |
| Sample type |
SRA |
| |
|
| Source name |
myocardial ischemia reperfusion with an early short-term T3-replacement (IRT3)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
developmental stage: Adult
Sex: male
tissue: cardiac
tissue subtype: left ventricle myocardial peri-infarct zone
|
| Treatment protocol |
24h after induction of cardiac IR, rats were subjected to 48h infusion with T3 at 3mg/Kg day (IR-T3 group) or its vehicle (IR-group), Sham operated rats were used as control
|
| Growth protocol |
Rats were housed in authorized Experimental Biomedical Centre of the CNR Research Area according to the national current regulations
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from heart specimens was extracted with the miRneasy mini kit (QIAGEN, Italy) as directed by the manufacturers’ instructions.
cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis (Invitrogen) and eluted into 300 µl elution buffer (Illumina) for at least 2 hours at room temperature, to enrich for molecules containing inserts in the range of 18–33 nt.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pool1_Index9_GATCAG_L004
smallRNAseq from dissected hearts
|
| Data processing |
Data extraction was performed using bcl2fastq-1.8.3, Read data were extracted in FastQ format
Sequenced reads were trimmed for 3' adaptor sequences.
Reads were aligned to mirBase v20.0 using mirExpress
Low counting miRNAs were filtered out and expression values were normalized for library size using estimateSizeFactors function of DESeq.
Genome_build: rattus pre-mirna mirBase v20
Supplementary_files_format_and_content: tab-delimited text file includes normalized read count per sample
|
| |
|
| Submission date |
Jun 20, 2018 |
| Last update date |
Jul 31, 2018 |
| Contact name |
Romina D'Aurizio |
| E-mail(s) |
[email protected]
|
| Organization name |
CNR
|
| Department |
IIT
|
| Street address |
via Moruzzi 1
|
| City |
Pisa |
| State/province |
PI |
| ZIP/Postal code |
56127 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE116046 |
Integrative analysis of differentially expressed genes and miRNAs predicts complex T3-mediated protective circuits in a rat model of cardiac ischemia reperfusion |
|
| Relations |
| BioSample |
SAMN09461855 |
