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Sample GSM4633028

Query DataSets for GSM4633028

Status

Public on Jun 23, 2020

Title

28d_2 pectoral muscle

Sample type

SRA

Source name

pectoral muscle

Organism

Columba livia

Characteristics

tissue: pectoral muscle
developmental stage: 28d

Treatment protocol

12 parent white king pigeons (6 male and 6 female at 2- year-old) and 24 squabs (mixed sex) were grouped into 3 stages (12 replicates for each stage): the age of 1 day (1d), 28 day (28d) and 2 years old (2yr). After weighing the body weight, pigeons were anaesthetized with ether and subsequently euthanized. Next,the pectoral muscle tissues from the same anatomical location were collected from pigeons. Subsequently, the samples for small RNA sequencing were stored frozen in liquid nitrogen and stored at −80◦C until RNA extraction,

Extracted molecule

total RNA

Extraction protocol

Total RNA was respectively extracted from frozen pectoral muscle samples with TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
The quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano Reagents Part 1 kit (Agilent Technologies, USA). Each development stage has three replicates that came from the three pigeons. Total RNA of each replicate was individually used for library construction. For each library, small RNA ranging from 10-45 nt in length was purified by polyacrylamide gel electrophoresis and ligated using proprietary adaptors. The modified small RNA was then reverse-transcribed to cDNA and amplified by PCR. Finally, libraries were sequenced by an Illumina Hiseq 2500 platform and generate 50 bp single-end reads.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Description

micRNAs from pectoral muscle in 28-day pigeon
identified miRNA reads count.txt

Data processing

the initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences were then mapped to the pigeon reference genome (Columba livia, ColLiv2, GenBank assembly accession: GCA_001887795.1) (https://www. ncbi.nlm.nih.gov/assembly/GCA _001887795.1) with stringent criteria (0 mismatch for full length) using Bowtie software.
Next, mappable reads were extended in the reference genome as predicted miRNA precursors. Only candidate precursors that perfectly matched to known pigeon (Columba livia) mature miRNAs annotated by miRBase (Release 22.0) were identified as known pigeon miRNAs.
Subsequently, to identify the conserved miRNAs, we performed alignments between remaining candidate precursors and seed sequences of mature miRNAs from chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and other mammals, allowing no mismatch.
Novel miRNAs were further predicted using the miRDeep2 core algorithm
Genome_build: Genome database:pigeon genome (assembly GCA_001887795.1); miRbase version: V22.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads

Submission date

Jun 22, 2020

Last update date

Jun 23, 2020

Contact name

Xun Wang

E-mail(s)

xunwang@sicau.edu.cn

Phone

+862882707606

Organization name

Sichuan agricultural university