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Sample GSM3963105

Query DataSets for GSM3963105

Status

Public on Jan 09, 2020

Title

Sample type

SRA

Source name

Whole milk

Organism

Bos taurus

Characteristics

breed: Holstein

Extracted molecule

total RNA

Extraction protocol

Total RNA were isolated from whole milk using RNA NOW kit (Ozyme) with overnight precipitation
Illumina TruSeq Small RNA Library Prep Kit

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 (https://forgemia.inra.fr/sylvain.marthey/paqmir/blob/master/paqmir_postprocess_quantifier/parse_miRDeep2_output.pl) to eliminate any redundancy between mature microRNAs by assigning them to the precursors in the following order of priority: 1) mature known in the bovine species, 2) mature known in another species then 3) mature predicted unknown. Additionally, microRNAs of the last two categories were faced with the new RumimiR database (v. June 2019) in order to identify ruminant microRNAs already described in literature but not in the last version of miRBase (v.22), and this information was included for the annotation of quantified microRNAs.
Genome_build: bosTau8

Submission date

Jul 22, 2019

Last update date

Jan 09, 2020

Contact name

Sandrine Le Guillou

E-mail(s)

sandrine.le-guillou@inrae.fr

Organization name

INRAE

Department

Animal Genetics