|
| Status |
Public on Jul 01, 2018 |
| Title |
94_S43_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
endometrium
|
| Organism |
Bos taurus |
| Characteristics |
week after calving: 9
cyclicity status: cycling no progesterone at week five after calving
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from endometrium using a Trizol-based method
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 |
| |
|
| 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 |
Dec 15, 2017 |
| Last update date |
Jul 01, 2018 |
| Contact name |
Matthew Lucy |
| Organization name |
University of Missouri
|
| Department |
Division of Animal Sciences
|
| Street address |
920 East Campus Drive
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE108163 |
Uterine microbiome in postpartum dairy cows: Associations with ovarian cyclicity and endometrial transcriptome at five and nine weeks after calving |
|
| Relations |
| BioSample |
SAMN08183018 |
| SRA |
SRX3475107 |
