|
| Status |
Public on Apr 01, 2014 |
| Title |
C16.17 |
| Sample type |
SRA |
| |
|
| Source name |
day 16 cyclic endometrium
|
| Organism |
Bos taurus |
| Characteristics |
day: 16
pregnancy_status: cyclic
|
| Treatment protocol |
Thirty-eight heifers were inseminated, and 16 were left as noninsemi- nated cyclic controls. Heifers were then randomly assigned to be slaughtered on day 13 or 16 of early pregnancy/estrous cycle corre- sponding to the initiation of conceptus elongation (day 13) and maternal recognition of pregnancy (day 16) in pregnant heifers, respectively.
|
| Growth protocol |
In brief, the estrus cycles of cross-bred beef heifers (predominantly Charolais and Limousin cross) were synchronized using a controlled internal drug release (CIDR) device (1.94 g pro- gesterone; InterAg, Hamilton, New Zealand) placed into the vagina for 8 days with intramuscular administration of a prostaglandin F2α analog (equivalent to 0.5 mg of PG, Estrumate; Shering-Plough Animal Health, Hertfordshire, UK) 3 days prior to CIDR removal. Only heifers detected in standing estrous were used (n = 54).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All reproductive tracts were processed <30 min post- slaughter, whereby the uterine horn ipsilateral to the CL was flushed with phosphate-buffered saline containing 5% fetal calf serum. In inseminated heifers, the presence of the conceptus was determined by examination under a stereomicroscope. Tissue was collected only from heifers from which a conceptus at the appropriate stage of development was recovered. After being flushed, the uterine horn ipsilateral to the CL was opened longitudinally, and 300 mg strips of endometrium (predominantly inter- caruncular tissue) were immersed in 1:5 wt/vol of RNAlater. This tissue was transported back to the laboratory on ice, stored at 4°C for 24 h, removed from RNAlater, and stored at <80°C prior to RNA extrac- tion.
RNA libraries were prepared for sequencing using standard Illumina protocols for single read libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Image analysis and base calling was carried out using Illumina IPAR1.01 software
Alignment to bt4 genome was carried out with Illumina ELAND software
Read counts for each transcript was generated by Illumina CASAVA software
Genome_build: bt4
Supplementary_files_format_and_content: raw counts for each transcript for each sample
|
| |
|
| Submission date |
Mar 31, 2014 |
| 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 |
GPL15750 |
| Series (1) |
| GSE56392 |
Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau |
|
| Relations |
| BioSample |
SAMN02712549 |
| SRA |
SRX504875 |
