|
| Status |
Public on May 01, 2018 |
| Title |
Foetus rep1 |
| Sample type |
SRA |
| |
|
| Source name |
heart - left ventricle
|
| Organism |
Cavia porcellus |
| Characteristics |
strain/background: Dunkin Hartley
age: Fetus, gestation day 67
tissue: heart, left ventricle
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Adult male and female guinea pigs (Dunkin Hartley; Envigo UK) were housed under standard 12 hour day/night cycles and fed ad libitum. Non-pregnant and time-mated term (day 66-67) pregnant guinea pigs were killed by anesthetic overdose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts isolated from the animals were immediately flushed with excess cardioplegic solution (glucose 227.5mM, mannitol 34.5mM, KCl 30mM, NaHCO3 25mM, pH 7.4) by retrograde perfusion via the aorta to clear all blood. The left ventricular walls were dissected out, frozen in liquid nitrogen and tissues stored until use at -80degC. Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing with standard Illumina protocols using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold, Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
235M2
|
| Data processing |
Alignment: start 2.5.2b
Normalised abundance: DESeq2
Genome_build: cavPor3
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited ASCII file.
Supplementary_files_format_and_content: normalisedcounts.csv: Comma-separated text file includes normalised counts.
|
| |
|
| Submission date |
Dec 21, 2017 |
| Last update date |
May 01, 2018 |
| Contact name |
Aurora Gomez-Duran |
| Organization name |
Cambridge University
|
| Department |
Department of Clinical Neurosciences
|
| Lab |
Mitochondrial Biology Unit
|
| Street address |
Welcome Trust/MRC Building
|
| City |
Cambridge |
| State/province |
Cambridge |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22346 |
| Series (1) |
| GSE108420 |
Transcriptomics analysis of guinea pig heart, fetus to adult progression |
|
| Relations |
| BioSample |
SAMN08225640 |
| SRA |
SRX3504113 |
