|
| Status |
Public on May 31, 2023 |
| Title |
CE5 |
| Sample type |
SRA |
| |
|
| Source name |
milk extracellular vesicles
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
group: Before initiation of feed restriction trial of high intensity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA-Seq librairies were generated from NA to 200ng of total RNA (or from --- ng of purified small RNA fraction) using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
After adapters cleaning and filtering for their size (17-28 nt) with Cutadapt, the RNA-seq data were analysed using miRDeep2 software, with bovine reference genome bosTau8 and miRBase release 22 (all species). The quantification results generated by the quantifier.pl miRDeep2 module were filtered with a custom perl script parse_miRDeep2_outputs.pl
Assembly: bosTau8
|
| |
|
| Submission date |
Jul 08, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
Sandrine Le Guillou |
| E-mail(s) |
sandrine.le-guillou@inrae.fr
|
| Organization name |
INRAE
|
| Department |
Animal Genetics
|
| Lab |
Animal Genetics and Integrative Biology
|
| Street address |
Domaine de Vilvert Bat.440
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL23295 |
| Series (1) |
| GSE207759 |
Milk microRNA variations in different milk compartments during feed restrictions of different intensities in dairy cows |
|
| Relations |
| BioSample |
SAMN29599696 |
| SRA |
SRX16086607 |
