GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM7102834

Query DataSets for GSM7102834

Status

Public on May 10, 2023

Title

Goat number 79 [C_079]

Sample type

SRA

Source name

Total RNA was extracted from milk EV of cows. There was 2 group of 5 cows and 4 goats

Organism

Capra hircus

Characteristics

day in milk: 26 +/- 9
cell type: milk-derived extracellular vesicle

Extracted molecule

total RNA

Extraction protocol

Milk-derived EVs were obtained by sucrose gradient ultracentrifugations. Then, total RNAs were isolated from EV samples by mirVana Total RNA Isolation Kit (Life Technologies) using Trizol LS Reagent (Ambion) in the firts step.
Small RNA-Seq librairies were generated from 100 ng of total RNA using NEBNext library generation kit (New England Biolabs INC.). Sequencing was performed using NewSeq 500 sequencing methodology (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified by 15 cycles to create cDNA constructs. Amplified cDNA constructs were size fractionated on a LabChip XT (Caliper Life Sciences) and a band representing adaptors and 15-40 bp insert excised using the manufacturer’s instructions. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis. the libraries were pooled in equimolar concentrations. The library pools were finally quantified again with qPCR and optimal concentration of the library pools used to generate the clusters on the surface of a flow cell before sequencing using NexSeq 500 sequencing methodology and reagents, according to the manufacturer instructions (Illumina).

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina NextSeq 500

Data processing

The vast majority of the data has a Q score greater than 30 (>99.9% correct)
Adapters were trimmed off. After, the read length distribution showed as expected main peak around 18-23 nt. representing microRNAs
Mapping was performed using bta and chi genome and annotation using miRBase 20
Assembly: bta and chi genome and annotation using miRBase 20
Supplementary files format and content: excel

Submission date

Mar 17, 2023

Last update date

May 10, 2023

Contact name

christine Leroux

E-mail(s)

christine.leroux@inrae.fr

Organization name

INRAE

Street address

Route de Theix