|
| Status |
Public on Sep 23, 2019 |
| Title |
R2-LP-FF_Biological_replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
Follicular fluid
|
| Organism |
Bos taurus |
| Characteristics |
gender: Female
condition: Postpartum
tissue: Follicular fluid extracellular vesicles
metabolic status: Late positive
weeks of postpartum: Week 9-10
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracellular vesicle isolation was performed using ultracentrifugation. Isolation of EV total RNA enriched for miRNA was done using an exosomal RNA isolation kit (Norgen Biotek Thorold, Canada).
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN Genomic Services, Hilden, Germany).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
R2-LP-FF
|
| Data processing |
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.). The FASTQ data were checked using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Trimming was done using Cutadapt (1.11) to extract information of adapter and UMI in raw reads. The output from cutadapt was used to remove adapter sequences and to collapse reads by UMI with inhouse script.
For mapping of the reads, Bowtie2 (2.2.2) software was used.
For the differential expression analysis, the EdgeR statistical (Bioconductor, http://bioconductor.org/) software package was used.
For normalization, the trimmed mean of M-values method based on log-fold and absolute gene-wise changes in expression levels between samples (TMM normalization) was used.
Genome_build: UMD3.1
Supplementary_files_format_and_content: CSV with average read count of each microRNA.
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Tsige Hailay |
| E-mail(s) |
thai@itw.uni-bonn.de
|
| Organization name |
University of Bonn
|
| Department |
Animal Breeding and Husbandry
|
| Street address |
Endenicher Allee 15
|
| City |
Bonn |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE129367 |
Differential expression profiles of extracellular vesicle-coupled miRNA in follicular fluid of cows at different metabolic status |
|
| Relations |
| BioSample |
SAMN11348545 |
| SRA |
SRX5645008 |
