|
| Status |
Public on Jun 15, 2012 |
| Title |
TCA610.1 |
| Sample type |
SRA |
| |
|
| Source name |
Theca cells of dominant follicle
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Theca
Stage: Selected
animaltype: Cow
animalid: 610.1
|
| Treatment protocol |
Selection group had their used CIDRs removed on the morning of Day 14 and were slaughtered. On the last ultrasound scan before slaughter all animals had a newly selected dominant follicle and a corpus luteum present. Animals assigned to the Differentiation and Luteinization groups received a luteolytic dose of PG on Day 13 and the CIDR was removed on the morning of Day 15 to accurately synchronise the follicular phase differentiation of selected dominant follicles. Animals assigned to the Differentiation group were then slaughtered on Day 16 between 24 and 30 h after CIDR removal and before any animals displayed estrus indicating the onset of the gonadotrophin surge. Animals assigned to the Luteinization group received an intramuscular injection of 5 ml GnRH 30 h post CIDR removal which induces a synchronised gondotrophin surge, and were slaughtered 18-22 h after the administration of GnRH (day 17) timed to occur before ovulation but after the onset of luteinisation.
|
| Growth protocol |
The estrous cycles of 16 Holstein-Friesian lactating cows and 17 nulliparous Holstein-Friesian dairy heifers (1.6 years ± 0.06; kept on the same farm) were pre-synchronized by insertion of a controlled intravaginal drug releasing device (CIDR) (containing 1.38g of progesterone) and a 2 ml intramuscular injection of a prostaglandin F2α anologue. Subsequent to detection of estrus, animals were treated with a used CIDR on Day 8 (Day 0 = observed estrus).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Theca.A.COW.TCA610.1.counts.txt; genome build: bt4
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
|
| |
|
| Submission date |
Dec 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul McGettigan |
| E-mail(s) |
pmcget02@gmail.com
|
| Organization name |
University College Dublin
|
| Department |
School of Agriculture, Food Science and Veterinary Medicine
|
| Lab |
Animal Genomics Laboratory
|
| Street address |
Veterinary Sciences Centre, UCD
|
| City |
Belfield |
| State/province |
Co Dublin |
| ZIP/Postal code |
Dublin 4 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL11153 |
| Series (1) |
| GSE34317 |
RNA-seq profiling of theca and granulosa tissue of dominant follicle at 3 stages of follicular development in cows and heifers. |
|
| Relations |
| SRA |
SRX110972 |
| BioSample |
SAMN00765072 |
