|
Status |
Public on Dec 13, 2016 |
Title |
E16-2 |
Sample type |
SRA |
|
|
Source name |
leg musle
|
Organism |
Gallus gallus |
Characteristics |
age: 16 embryo age breeds: Xinghua chicken Sex: female
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were isolated by Trizol reagent (Invitrogen) and then Ribosomal RNA (rRNA) was removed from the total RNA using Epicentre Ribo-ZeroTM rRNA Removal Kit. Total RNA samples (5 μg) were treated with the Epicentre RibozeroTM rRNA removel kit (Epicenter) to remove rRNA. RNA-seq libraries were prepared using the TruSeq® RNA LT Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
Ribosomal RNA removed
|
Data processing |
Illumina Casava1.7 software used for basecalling. For all generated raw reads, adaptor sequences and low quality reads were filtered with the Trim Galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Sequenced reads were assemblyed by Cufflinks, and mapped to chicken genome using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml) and Tophat (Trapnell et al., Bioinformatics, 2009). LncRNAs were annoted using CPC, HMMER+pfam and CPAT software. The expression levels of the transcripts are expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values Genome_build: Gallus_gallus.Galgal4.73 Supplementary_files_format_and_content: Microsoft Excel files include FPKM values for each sample.
|
|
|
Submission date |
Dec 08, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Zhenhui Li |
E-mail(s) |
hunanndlzh@163.com
|
Organization name |
South China Agricultural University
|
Street address |
Tianhe District Wushan road
|
City |
Guangzhou |
ZIP/Postal code |
510642 |
Country |
China |
|
|
Platform ID |
GPL19005 |
Series (1) |
GSE91060 |
Genome-wide analysis of long non-coding RNA (lncRNA) profiles in leg muscle of Xinghua Chickens. |
|
Relations |
BioSample |
SAMN06125003 |
SRA |
SRX2406015 |