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Sample GSM5086316

Query DataSets for GSM5086316

Status

Public on Feb 17, 2021

Title

submandibular glands, B5

Sample type

SRA

Source name

submandibular gland

Organism

Capra hircus

Characteristics

tissue: submandibular gland
age: 12 month

Treatment protocol

All goats were raised under the same conditions, including natural lighting and free access to food.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from the submandibular salivary gland tissues using TRIzol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina miRNA protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Raw reads were filtered with FastQC: Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); removing reads without 3’adapters; removing reads containing 5’adapters; removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; removing reads containing ployA in small RNA fragment; removing reads shorter than 18nt
Applied with Bowtie, we aligned our clean reads with small RNAs in GeneBank database (Release 209.0) and Rfam database (11.0) to identify and remove rRNA, scRNA, snoRNA, snRNA and tRNA. We also mapped our clean reads with goat reference genome (Capra hircus ARS1), and those reads mapped to exons, introns and repeat sequences were removed. To identify known miRNAs, we mapped clean reads with miRBase database (Release 22)
All of the unmapped reads were applied for novel miRNA identification according to their genome positions and hairpin structures predicted by software Mireap_v0.2. The parameters of Mireap_v0.2 were settled as follows: Minimal miRNA sequence length is 18nt, maximal miRNA sequence length is 26nt, minimal miRNA reference sequence length is 20nt, maximal miRNA reference sequence length is 24nt, minimal depth of Drosha/Dicer cutting site is 3, maximal copy number of miRNAs on reference is 20, maximal free energy allowed for a miRNA precursor is 18 kcal/mol, maximal space between miRNA and miRNA* is 35nt, minimal space between miRNA and miRNA* is 14nt, maximal bulge between miRNA and miRNA* is 4nt, maximal asymmetry of miRNA/miRNA* duplex is 5nt, flank sequence length of miRNA precursor is 10nt.
Genome_build: Capra hircus ARS1
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

Submission date

Feb 16, 2021

Last update date

Feb 17, 2021

Contact name

Chao Tianle

E-mail(s)

chaotianle@sdau.edu.cn

Phone

15153876133

Organization name

6/5000 Shandong Agricultural University