|
| Status |
Public on Aug 25, 2012 |
| Title |
endometrium 30 days postpartum 3 |
| Sample type |
SRA |
| |
|
| Source name |
Endometrial Biopsy
|
| Organism |
Bos taurus |
| Characteristics |
time: 30 days postpartum
tissue: endometrium
breed: mixed
histological grade of inflammation: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen endometrial tissue was homogenised and total RNA was extracted using Trizol. The Illumina mRNA Sequencing Sample Preparation Kit [2009] was used to construct libraries. Poly-T oligo-attached magnetic beads allowed the isolation and pruification of poly-A tailed mRNA which was fragmented, converted to double stranded cDNA, sequencing primers and adapters were attached. 300bp fragments were then size selected for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Base-calling done with CASAVA 1.4
mRNA-Seq reads were aligned to the Btau4.0 genome using TopHat (Settings: -r 200 --solexa1.3-quals --library-type fr-unstranded --segment-length 20 --segment-mismatches 1)
HtSeq-Count summarised the number of genes per gene (settings: mode = union)
Genome_build: Btau_4.0.62
Supplementary_files_format_and_content: Tab delimited txt files. Row 1 has ENSEMBL gene IDs and row 2 has the raw number of reads mapping to each gene.
|
| |
|
| Submission date |
Aug 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Cathriona Foley |
| Organization name |
Teagasc
|
| Street address |
Grange
|
| City |
Dunsany |
| ZIP/Postal code |
Meath |
| Country |
Ireland |
| |
|
| Platform ID |
GPL11153 |
| Series (1) |
| GSE40312 |
Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows |
|
| Relations |
| SRA |
SRX180581 |
| BioSample |
SAMN01125822 |
