|
| Status |
Public on Oct 23, 2024 |
| Title |
SAN_4 |
| Sample type |
SRA |
| |
|
| Source name |
Follicular fluid
|
| Organism |
Equus caballus |
| Characteristics |
tissue: Follicular fluid
cell type: Extracellular Vesicles
breeding season: Spring anovulatory
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For EV isolation, 2 ml of pre-centrifuged follicular samples were subjected to an ultracentrifugation procedure at 120,000 xg for 70 min at 4 OC using the Beckman SWTi55 rotor. The EVs pellet was washed with sterile PBS and then centrifuged again at 120,000 ×g for 70 min. Finally, EVs were resuspended in 500 µL of PBS and stored in −80 °C until further characterization and analysis.
Small-RNA libraries were prepared for next-generation sequencing (NGS) using a TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
|
| |
|
| 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 Equus caballus reference genome (EquCab3.0) Bowtie2 (2.2.2)
Mapped reads were used for annotation against equine 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: EquCab3.0
Supplementary files format and content: xlsx file include CPM values for each sample
|
| |
|
| Submission date |
Dec 02, 2023 |
| Last update date |
Oct 23, 2024 |
| 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 |
GPL26749 |
| Series (1) |
| GSE249220 |
Seasonal variations of extracellular vesicle-coupled microRNAs in equine follicular fluid |
|
| Relations |
| BioSample |
SAMN38600126 |
| SRA |
SRX22720523 |
