|
| Status |
Public on Jan 04, 2018 |
| Title |
Female CTRL Rat 4- 24 months old |
| Sample type |
SRA |
| |
|
| Source name |
Left Ventricle
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: F-344 Brown/Norway Rat
tissue: Left Ventricle
age: 24 months
Sex: Female
treatment: CTRL
|
| Treatment protocol |
Rats were treated with control (Sodium Acetate) or RLX (400 ug/kg/day) for 14 days via subcutaneous osmotic mini pumps.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Preparation was performed using TruSEQ Standard Total RNA Sample Preparation Kit (Illumia, San Diego, CA) according to manufactuers instructions.
Following removal of ribosomal sequences, RNA was fragmented for 8 minutes and reverse transcription performed. Double stranded cDNA was subjected to 3’ adenylation and ligation of sequencing adapters. Sequencing was carried out on a NextSeq 500 (Illumina) for 2 x 75 bp paired end reads. Loading concentration was 1.2-1.4 pM.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file header: GS22
processed data file: Female_24_month_and_9_month_Controls.xlsx
processed data file: Female_24_month_Control_and_RLX_treated.xlsx
|
| Data processing |
Fastq files were uploaded into Biomedical Genomics Workbench, v.3.0.1
Base pair reads were matched to the rat reference sequence (rattus_norvegicus_ensembl_v79)
Gene expression changes were based on total count differences between groups.
Comparisons between groups were performed on Biomedical Genomics Workbench 3.0.1 between young and aged male ctrls, aged RLX treated and aged ctrl males, young and aged female ctrls, aged RLX treated and aged ctrl females
For data imported into Ingenuity Pathway Analysis, filters were applied to include only genes with absolute fold changes greater than 1.5 and an FDR < 0.05.
Genome_build: rattus_norvegicus_ensembl_v79
Supplementary_files_format_and_content: Female 24 month and 9 month Controls: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Female 24 month Control and RLX treated: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Male 24 month and 9 month Controls: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
Supplementary_files_format_and_content: Male 24 month Control and RLX treated: Expression browser performed in Biomedical Genomics Workbench 3.0.1 to determine expression changes between groups. Data exported to Excel.
|
| |
|
| Submission date |
Oct 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Martin |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pittsburgh
|
| Department |
Bioengineering
|
| Lab |
Salama
|
| Street address |
3550 Terrace St
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE106377 |
Relaxin reverses inflammatory and immune signals in aged hearts |
|
| Relations |
| BioSample |
SAMN07959873 |
| SRA |
SRX3347197 |
