|
| Status |
Public on Dec 13, 2016 |
| Title |
E11-1 |
| Sample type |
SRA |
| |
|
| Source name |
leg musle
|
| Organism |
Gallus gallus |
| Characteristics |
age: 11 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 |
SAMN06125081 |
| SRA |
SRX2406012 |
