|
| Status |
Public on Feb 24, 2020 |
| Title |
pregnant uterus miRNA rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
uterus
|
| Organism |
Equus caballus |
| Characteristics |
tissue: uterus
Stage: pregnant
|
| 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 |
Total RNA was extracted from the UF and the YS fluid samples for miRNA analysis, using the miRNeasy Serum/Plasma kit (Qiagen), according to the manufacturers' instructions. 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.
MicroRNA sequencing libraries were constructed and size-selected with the TailorMix miRNA Sample Preparation Kit V2 (SeqMatic, Fremont, CA, USA) using 100 ng total RNA and amplified by 18 PCR cycles.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
P3BmiRNA
novel_mature.fa
novel_precursor.fa
result_mature.csv
result_novel_mature.csv
result_novel_precursor.csv
|
| Data processing |
Adapter trimming and removal of reads shorter than 17 bp, having a quality score lower than 20 or containing any ambiguities, was done using cutadapt (v1.11).
Feature counting, identification of known miRNAs and prediction of putative novel miRNA were done using the miRPro pipeline.
MicroRNA data from miRBase (release 22) and the corresponding annotated horse genome (EquCab2.0) were used as a reference. All mammalian data in miRBase was used for the prediction of novel miRNA.
Genome_build: EquCab2.0
Supplementary_files_format_and_content: Comma separated count files. Fasta files of the predicted miRNAs.
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Laurentijn Tilleman |
| Organization name |
Ghent University
|
| Street address |
Ottergemsesteenweg 460
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL27862 |
| Series (2) |
| GSE141443 |
Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? [miRNA-seq] |
| GSE141450 |
Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? |
|
| Relations |
| BioSample |
SAMN13480451 |
| SRA |
SRX7267361 |
