|
| Status |
Public on Jan 04, 2013 |
| Title |
8-178 |
| Sample type |
SRA |
| |
|
| Source name |
Cervix
|
| Organism |
Bos taurus |
| Characteristics |
Stage: Luteal
animaltype: Heifer
animalid: 8-178
timepoint: 6
|
| Treatment protocol |
Cervical tissues were collected at slaughter from heifers 12h after CIDR removal (Group 1: CIDR + 12 h, n = 6), 24h after CIDR removal (Group 2: CIDR + 24 h, n = 6), at the onset of estrus (Group 3: Estrus, n = 4), 12 h after the onset of estrus (Group 4: estrus + 12 h, n = 5), 48 h after the onset of estrus (Group 5: Estrus+48h, n = 4) and on day 7 after the onset of estrus (Group 6: Luteal phase, n = 5).
|
| Growth protocol |
The estrous cycles of Limousin heifers (n = 30) were synchronized by insertion of a controlled internal drug release (CIDR) device (1.94 g progesterone; Pfizer Animal Health) placed into the vagina for 8 days. A 0.5 mg intramuscular injection of a prostaglandin F2α (PG) analogue (PG, Estrumate, Shering-Plough Animal Health, Hertfordshire, UK) was administered 1 day before CIDR removal. Heifers were checked for standing estrus and only those exhibiting estrus (Day 0) were used.
|
| 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 |
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.
Genome Build:
cervix_Luteal_14.counts.txt: bt4
|
| |
|
| Submission date |
May 24, 2012 |
| 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) |
| GSE38225 |
RNA-seq profiling of the bovine cervix at 6 timepoints during the peri-oestrus period. |
|
| Relations |
| SRA |
SRX149490 |
| BioSample |
SAMN00998370 |
