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| Status |
Public on May 30, 2024 |
| Title |
D2 |
| Sample type |
SRA |
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| Source name |
Follicular Fluid
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| Organism |
Ceratotherium simum |
| Characteristics |
tissue: Follicular Fluid
cell type: Extracellular Vesicles
follicle stage: Dominant
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| Extracted molecule |
total RNA |
| Extraction protocol |
EVs were isolated using the dual-ended approach of ultracentrifugation followed by precipitation and elution through size exclusion chromatography columns. Initially, in three technical replicates, frozen-thawed collections containing 2 mL of follicular fluid aspirate from individual animals were subjected to an initial ultracentrifugation using an SW 55Ti rotor on the Optima XE-90 Ultracentrifuge (Beckman Coulter; Pasadena, CA, USA.) system at 120,000 xg for 70 min at 4°C, Pelletized EVs were then washed using 3 mL of Dulbecco’s Phosphate Buffered Saline without calcium and magnesium chloride (DPBS (1X)) (Sigma-Aldrich; St. Louis, MO, USA.) and ultracentrifuged once more under the same parameters. Following ultracentrifugation, washed EV pellets were resuspended in Exo-spin™ Buffer and left to precipitate overnight at 4°C prior to being processed through Exo-spin™ mini columns (CELL guidance systems; St. Louis, MO, USA.) according to the manufacturer’s protocol. Ensuing 180 µL EV aliquots were then stored at -80°C for RNA extraction.
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.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Reads were used for annotation against equine, bovine, and human 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: mirBase database (release 22), against equine, bovine, and human mature and precursor miRNAs
Supplementary files format and content: xlsx file include CPM values for each sample
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| Submission date |
Oct 25, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
Ahmed Gad |
| E-mail(s) |
ahmed.y.gad@agr.cu.edu.eg
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| Organization name |
Colorado State University
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| Department |
Biomedical Sciences
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| Lab |
ARBL
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| Street address |
3107 Rampart Rd
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| City |
Fort Collins |
| State/province |
Colorado |
| ZIP/Postal code |
80521 |
| Country |
USA |
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| Platform ID |
GPL33869 |
| Series (1) |
| GSE246260 |
Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum) |
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| Relations |
| BioSample |
SAMN37985566 |
| SRA |
SRX22229177 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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