|
| Status |
Public on Aug 17, 2018 |
| Title |
U-2-0-146-29mm |
| Sample type |
SRA |
| |
|
| Source name |
Endometrium
|
| Organism |
Bos taurus |
| Characteristics |
treatment: AI
conceptus sex: Female
tissue: Endometrium
|
| Treatment protocol |
Explants (endometrial side up) were cultured for 6 h with: (i) RPMI medium alone (Control; n=6 explants); (ii) RPMI medium containing 100 ng/mL of recombinant ovine IFNT (n=6 explants); (iii) a Day 15 conceptus derived from the transfer of in vivo-derived blastocysts (AI, n=4 explants) in RPMI media; or (iv) a Day 15 conceptus derived from the transfer of in vitro produced blastocysts (IVF, n=7 explants) in RPMI media. Explants were incubated in 5% CO2 and air at 38.8°C during treatment. Following treatment, explants were immediately snap frozen in liquid nitrogen until total RNA extraction.
|
| Growth protocol |
Following dissection with an 8-mm biopsy punch, intercaruncular endometrial explants (50-80 mg) were washed in Hank’s Balanced Salt Solution (HBSS; Gibco, ThermoFisher Scientific) containing 1% ABAM before placement in culture wells (4-well plate) containing 1 mL of Roswell Park Memorial Institute (RPMI) medium (Gibco, ThermoFisher Scientific) with 1% ABAM. Explants were cultured endometrial side up in 5% CO2 and air at 38.8°C for 1 to 5 h before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from ~50 mg of endometrial explant tissue using Trizol reagent (Invitrogen) per the manufacturer´s instructions. On-column RNA clean-up was performed using the Qiagen mini kit (Qiagen).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample18
readcounts.txt
|
| Data processing |
The raw sequences (fastq) were subjected to adapter removal and quality trimming using fqtrim (https://ccb.jhu.edu/software/fqtrim/).
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/) .
To produce a global gene annotation file (GTF) for comprehensive quantification of gene expressions across the samples, the sorted binary alignment maps of sequence reads from each sample were assembled to generate transcriptomes those were then merged, along with the gene annotations from reference genome assembly.
The transcript assembly step was accomplished using the software ‘Stringtie’ (https://ccb.jhu.edu/software/stringtie/) .
The merged global transcriptome was then used in Stringtie to quantify transcript abundance of each sample. Differential expression analysis between sample groups were performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.
|
| |
|
| Submission date |
Aug 16, 2018 |
| Last update date |
Aug 17, 2018 |
| Contact name |
PATRICK LONERGAN |
| E-mail(s) |
pat.lonergan@ucd.ie
|
| Organization name |
University College Dublin
|
| Street address |
Belfield
|
| City |
Dublin 4 |
| ZIP/Postal code |
D04 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE118672 |
Interferon tau-dependent and independent effects of the bovine conceptus on the endometrial transcriptome: effect of conceptus origin and sex |
|
| Relations |
| BioSample |
SAMN09844538 |
| SRA |
SRX4561289 |
