|
| Status |
Public on Jun 23, 2023 |
| Title |
S_EV1 |
| Sample type |
SRA |
| |
|
| Source name |
Seminal Plasma
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: Seminal Plasma
cell type: Extracellular Vesicles
group: Sub-fertile
breed: California x New Zealand white rabbits
|
| Extracted molecule |
total RNA |
| Extraction protocol |
EVs were isolated from SP groups (3 biological replicates/group; 2.5 mL SP/replicate) using Ultracentrifugation and PURE-EV® (HansaBioMed Life Sciences) size exclusion chromatography (SEC). Total RNA was isolated from EV samples using Trizol and miRNeasy Micro Kit.
Small-RNA libraries were prepared using QIAseq miRNA Library Kit
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Oryctolagus cuniculus reference genome (OryCun2.0) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against rabbit mature and precursor miRNAs listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization) and presented as TMM-adjusted Counts Per Million (CPM)
The differential expression analysis was done using the DESeq2 statistical software package
Assembly: OryCun2.0
Supplementary files format and content: xlsx file include CPM values for each sample
|
| |
|
| Submission date |
Jul 23, 2022 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Ahmed Gad |
| E-mail(s) |
ahmed.y.gad@agr.cu.edu.eg
|
| Organization name |
Colorado State University
|
| Department |
Biomedical Sciences
|
| Lab |
ARBL
|
| Street address |
3107 Rampart Rd
|
| City |
Fort Collins |
| State/province |
Colorado |
| ZIP/Postal code |
80521 |
| Country |
USA |
| |
|
| Platform ID |
GPL26786 |
| Series (1) |
| GSE209607 |
Identification of specific miRNAs in the seminal plasma extracellular vesicles from fertile and subfertile rabbit bucks |
|
| Relations |
| BioSample |
SAMN29921457 |
| SRA |
SRX16533944 |
