|
| Status |
Public on Jun 22, 2017 |
| Title |
E16-1 |
| Sample type |
SRA |
| |
|
| Source name |
leg muscle
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: leg muscle
age: E16 embryo age
breed: Xinghua chicken
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from two embryonic and one post hatch chick leg muscle using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
miRNA 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 |
| |
|
| Description |
RNase R treated and ribo- RNAs
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences and low quality reads were filtered with the Fastx-Toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/) and Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Sequenced reads were assembled by Cufflinks, and mapped to chicken genome using Bowtie software (http://bowtie-bio.sourceforge.net /index.shtml) and Tophat (Trapnell et al., Bioinformatics, 2009).
Annotating high confidence miRNA using deep sequencing data (Kozomara A, Nucleic Acids Res 2014)
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: Excel file with abundance measurements. A fasta file with the novel miRNA sequences is available on the series record.
|
| |
|
| Submission date |
Jun 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Endashaw Jebessa Bekele |
| E-mail(s) |
2059118041@qq.com
|
| Phone |
+86-13249168535
|
| Organization name |
South China Agricultural University
|
| Department |
Animal Genetics, Breeding and Reproduction
|
| Lab |
Chicken Genetics, Breeding and Reproduction
|
| Street address |
Wushan street,Tianhe district
|
| City |
Guangzhou |
| State/province |
Guangduong |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL19005 |
| Series (1) |
| GSE100321 |
Deep Sequencing Analysis of miRNAs Expression in leg muscle of Xinghua Chicken |
|
| Relations |
| BioSample |
SAMN07264912 |
| SRA |
SRX2941882 |
