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Sample GSM4648415

Query DataSets for GSM4648415

Status

Public on Sep 08, 2020

Title

E131

Sample type

SRA

Source name

Breast muscle

Organism

Anas platyrhynchos

Characteristics

strain: Shanma duck
phenotype: myoblasts didn't differentiate
age: embryo 13 days
group: E13

Treatment protocol

Breast muscle samples of 15 ducks were collected every 3 days during E10 to 1-day post hatch (E10, E13, E16, E19, E22 and 1-day post hatch), quick-frozen by liquid nitrogen and stored at -80 °C until RNA extraction.

Growth protocol

A total of 120 hatching eggs of Shanma ducks with same genetical background were obtained from Jiangxi Tianyun duck breeding farm (Nanchang, Jiangxi), and incubated in the incubator (Keyu, Shandong, China) at 37.2 °C, with 60 ± 10% humidity.

Extracted molecule

total RNA

Extraction protocol

Total RNAs of six samples were extracted and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0. All samples were kept at -80 °C.
Libraries were prepared for sequencing using standard Illumina protocols

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Data processing

Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design. The significance threshold was set to be 0.01 and 0.05 in each test.
To predict the genes targeted by most aboundant miRNAs, two computational target prediction algorithms (TargetScan 50 and Miranda 3.3a) were used to identify miRNA binding sites. Finally, the data predicted by both algorithms were combined and the overlaps were calculated. The GO terms and KEGG Pathway of these most aboundant miRNAs, miRNA targets were also annotated.
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/anas_platyrhynchos_platyrhynchos/dna/
Supplementary_files_format_and_content: abundance measurements

Submission date

Jul 01, 2020

Last update date

Sep 08, 2020

Contact name

Biao Chen

E-mail(s)

chenbiao@jxau.edu.cn

Phone

18931507508

Organization name

Jiangxi Agricultural University