|
| Status |
Public on Aug 15, 2018 |
| Title |
Cont-day13 (#5-140) |
| Sample type |
SRA |
| |
|
| Source name |
Endometrium
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Contra uterus horn
time: pregnancy day13
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted from ~100 mg of endometrial homogenate using Trizol reagent (Invitrogen, Carlsbad, CA) per the manufacturer´s instructions. On-column DNase digestion and 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 |
S34
|
| Data processing |
Raw sequences (fastq) were subjected to quality control using windowed adaptive quality triming approach implemented in fqtrim (https://ccb.jhu.edu/software/fqtrim/).
Read quallity was checked by Fastqc and quality control was performed by fqtrim.
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/).
Read counts mapping to each gene were determined from the mapping data using FeatureCounts
Differential expression analysis between sample groups was performed by robustly fitting the expression data to a generalized linear model using edgeRrobust
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.
|
| |
|
| Submission date |
Aug 14, 2018 |
| Last update date |
Aug 15, 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) |
| GSE118507 |
Do differences in the endometrial transcriptome between uterine horns ipsilateral and contralateral to the corpus luteum influence conceptus growth to Day 14 in cattle? |
|
| Relations |
| BioSample |
SAMN09829862 |
| SRA |
SRX4551166 |
