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| Status |
Public on Nov 30, 2020 |
| Title |
T12_1 |
| Sample type |
SRA |
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| Source name |
Myocardium
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Myocardium
strain: Sprague-Dawley
treatment: 12wk post op MI+TRD surgery
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| Treatment protocol |
Rats were subjected to an MI surgery (left thoracotomy and ligation of the left coronary artery) or an MI surgery followed by a second surgery to implant the TRD device, and followed until 12 weeks
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Myocardial tissue was section, snap frozen in liquid nitrogen and stored at -80 degress celcius. RNA was harvested using the miRNeasy mini kit. RNA sequencing was performed using the Illumina platform (Novogene).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Partek Flow, version rn6 rat reference genome, was used to map reads.
Mapped reads were quantified using the RefSeq transcripts 2019-02-02 annotation, using the Partek E/M method using GSA to compare each experimental group against Sham
Data were filtered using the following specifications: p≤0.05 and 2 ≤ fold change ≤ -2.
Functional enrichment analysis was performed using Protein Analysis Through Evolutionary Relationships (PANTHER version 15), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, to identify molecular and biochemical pathways
Genome_build: rn6
Supplementary_files_format_and_content: The processed data files is a text file (.txt) and contain normalized counts for each feature for each individual sample
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| Submission date |
Apr 26, 2020 |
| Last update date |
Nov 30, 2020 |
| Contact name |
Muralidhar Padala |
| E-mail(s) |
spadala@emory.edu
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| Organization name |
Emory University
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| Street address |
380B Northyards Blvd NW
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30313 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE149364 |
RNA sequencing of rodent myocardial tissue when subjected to a myocardial infarction (MI) or an MI and a surgical device (TRD) for 12 weeks. |
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| Relations |
| BioSample |
SAMN14732925 |
| SRA |
SRX8177662 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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