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SRX22229176: GSM7865816: D1; Ceratotherium simum; miRNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 24.2M spots, 1.2G bases, 369.7Mb downloads

External Id: GSM7865816_r1
Submitted by: ARBL, Biomedical Sciences, Colorado State University
Study: Mapping the follicle-specific regulation of extracellular vesicle-mediated microRNA transport in the southern white rhinoceros (Ceratotherium simum simum)
show Abstracthide Abstract
Efforts to implement effective assisted reproductive technologies (ART) to extricate the northern white rhinoceros (NWR; Ceratotherium simum cottoni) from extinction, could be unconventionally offset from studies carried out using the southern white rhinoceros (Ceratotherium simum simum) as a relative model species. The bi-directional communication and critical transport of regulatory molecules controlling follicular growth and oocyte development are in part mediated through extracellular vesicles (EVs), which encompass a highly conserved and advanced paracrine signaling mechanism important in shuttling unique cargo such as microRNAs (miRNAs). In this study, critical miRNAs for follicular development were identified, proposing novel approaches using EV-mediated miRNA to possibly improve the in vitro technologies outcome in a multitude of species. Overall design: Two southern white rhinoceros females (n=2) were stimulated and utilized for transrectal OPU, facilitating the in vivo collections of follicular fluid aspirate from follicles of distinct size. Prior to ultrasound-guided ablation of follicles, follicles were assigned to predetermined categories based on their established diameter: growing (G; 11-17mm), dominant (D; 18-29mm), and pre-ovulatory (P; 30-34mm). Follicular fluids were used for EV isolation from which total RNA were isolated and smallRNA sequencing were performed.
Sample: D1
SAMN37985567 • SRS19284121 • All experiments • All runs
Library:
Name: GSM7865816
Instrument: Illumina NovaSeq 6000
Strategy: miRNA-Seq
Source: TRANSCRIPTOMIC
Selection: size fractionation
Layout: SINGLE
Construction 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.
Runs: 1 run, 24.2M spots, 1.2G bases, 369.7Mb
Run# of Spots# of BasesSizePublished
SRR2652574724,207,8601.2G369.7Mb2024-05-30

ID:
30187825

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