|
| Status |
Public on Feb 24, 2020 |
| Title |
cyclic uterus mRNA rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
uterus
|
| Organism |
Equus caballus |
| Characteristics |
tissue: uterus
Stage: cyclic
|
| Treatment protocol |
cyclic mares: no treatment, pregnant mares: inseminated and confirmed to be pregnant
|
| Growth protocol |
Samples were collected from cycling or pregnant mares 13 days after ovulation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction from the B and the E tissue samples, the RNeasy Mini Kit (Qiagen) was combined with the RNeasy MinElute Cleanup Kit (Qiagen) in order to extract both small RNAs and larger RNAs (>200 nt) separately from the same tissue sample for mRNA- and miRNA-Sequencing respectively.
1 µg of RNA was used to perform an Illumina sequencing library preparation using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol. During library preparation, 12 PCR cycles were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed using cutadapt version 1.11 to remove the Illumina adaptor sequence.
The trimmed reads were mapped against the equine EquCab 2.80 reference genome using CLC genomics workbench version 9.0.1 (CLC).
Count tables were made by counting the reads that mapped against the genes defined by the Ensembl EquCab 2.80 Gene transfer format file and exported from CLC.
Genome_build: EquCab 2.80
Supplementary_files_format_and_content: comma separated values files including Gene counts and Gene ID
|
| |
|
| Submission date |
Dec 03, 2019 |
| Last update date |
Feb 25, 2020 |
| Contact name |
Laurentijn Tilleman |
| Organization name |
Ghent University
|
| Street address |
Ottergemsesteenweg 460
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21401 |
| Series (2) |
| GSE141360 |
Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? [RNA-seq] |
| GSE141450 |
Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? |
|
| Relations |
| BioSample |
SAMN13471466 |
| SRA |
SRX7262487 |
