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Sample GSM6068148

Query DataSets for GSM6068148

Status

Public on Aug 31, 2022

Title

Sample type

SRA

Source name

milk

Organism

Bos taurus

Characteristics

tissue: milk
group: clinical
cell type: extracellular vesicles

Extracted molecule

total RNA

Extraction protocol

Small RNA was extracted from milk EVs using the miRNeasy Mini kit (Qiagen)，3 ug of total RNA was used for the construction of sequencing libraries.
3μg of total RNA was ligated with sequencing adapters with TruseqTM Small RNA sample prep Kit (Illumina, San Diego, CA, USA).

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

HiSeq X Ten

Data processing

Low-quality bases (Sanger base quality of < 20) of the 3’ end were trimmed using in-house perl scripts, and then the sequencing adapters were removed with the fastx toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/).
All identical sequences of sizes ranging from 18 to 32 nt were counted and eliminated from the initial data set. Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) was used to annotate the chromosomal location against the reference genome data.
Through a BLAST search of the miRbase, version 22.0 (http://www.mirbase.org/), the perfectly matched sequences were used to count and analyze the known miRNA expression profile. Then the assembled unique sequences were used for a BLAST search of the Rfam database, version 12.3 (http://rfam.sanger.ac.uk/), to remove non-miRNA sequences (rRNA, tRNA, snoRNA, etc.).
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miRDeep2 were integrated to predict novel miRNA. At the same time, in-house scripts were used to obtain the identified miRNA base bias on the first position with certain length and on each position of all identified miRNA.
The expression level of each miRNA was calculated according to the transcripts per million reads (TPM) method. Significant differently expressed (DE) miRNAs were extracted with |log2FC| >1 and P adjust < 0.05 by edgeR.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

Submission date

Apr 26, 2022

Last update date

Aug 31, 2022

Contact name

Mengling Wang

E-mail(s)

wangmengling0@gmail.com

Organization name

Institute of Animal Science, Chinese Academy of Agricultural Sciences

Lab

State Key Laboratory of Animal Nutrition