|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Sep 08, 2020 |
Title |
E192 |
Sample type |
SRA |
|
|
Source name |
Breast muscle
|
Organism |
Anas platyrhynchos |
Characteristics |
strain: Shanma duck phenotype: most myoblasts have differentiated age: embryo 19 days group: E19
|
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
|
Street address |
Zhimin street, Jingkai district
|
City |
Nanchang |
ZIP/Postal code |
330045 |
Country |
China |
|
|
Platform ID |
GPL22591 |
Series (1) |
GSE153629 |
Genome-wide microRNA profiling and target gene prediction in different embryonic muscle developmental stage of duck breast |
|
Relations |
BioSample |
SAMN15415388 |
SRA |
SRX8646750 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|