|
| Status |
Public on Oct 21, 2016 |
| Title |
JINDING rep8 |
| Sample type |
SRA |
| |
|
| Source name |
breast muscle or Pectoral muscle
|
| Organism |
Anas platyrhynchos |
| Characteristics |
breed: Jingding
tissue: pectoral muscle
age: 5 days post-hatching
|
| Extracted molecule |
total RNA |
| Extraction protocol |
eighteen polyA mRNA-seq libraries, including nine from Gaoyou duck PM and nine from Jingding duck PM,RNA was harvested using Trizol reagent.Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the Construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time
Genome_build: ftp://ftp.ensembl.org/pub/release-80/fasta/anas_platyrhynchos/dna/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Li hui fang |
| E-mail(s) |
zhuch_1304428@126.com
|
| Organization name |
Jiangsu Institute of Poultry Science
|
| Street address |
No.58 Cangjie Rd
|
| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225125 |
| Country |
China |
| |
|
| Platform ID |
GPL22591 |
| Series (1) |
| GSE88971 |
Deep RNA Sequencing of Pectoralis Muscle Transcriptomes during Late-term Embryonic to Neonatal Development in Indigenous Chinese Duck Breeds |
|
| Relations |
| BioSample |
SAMN05929770 |
| SRA |
SRX2254025 |
