|
| Status |
Public on Mar 31, 2017 |
| Title |
Jinding rep4 |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Anas platyrhynchos |
| Characteristics |
breed: Jinding
tissue: ovary
age: 340 days
egg production: high
|
| Treatment protocol |
The number of eggs of each duck was recorded daily. The laying rate of ducks higher than 99% was defined as high egg production group(HEP), and the laying rate of ducks lower than 85% was defined as low egg production group(LEP).
|
| Growth protocol |
Jinding ducks were obtained from Jiangsu Gaoyou Duck Group, Yangzhou, Jiangsu, China. These ducks were chosen from half-sib family, of same age and feeding condition. The ducks were raised to 340 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ducks ovaries were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TruSeq Stranded mRNA LTSample Prep Kit (Illumina,USA) was used with 4 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 ploy-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 v2.0.9.
FPKM 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(Mortazavi et al., 2008)
Genome_build: BGI_duck_1.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.fna.gz)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Dec 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
tao zhi yun |
| E-mail(s) |
zhiyun2@126.com
|
| Phone |
051485599199
|
| Organization name |
jinagsu lnstitute of Poultry Science
|
| Street address |
Cangjie road NO.58
|
| City |
Yangzhou |
| ZIP/Postal code |
225125 |
| Country |
China |
| |
|
| Platform ID |
GPL22591 |
| Series (1) |
| GSE92253 |
Transcriptomic analysis of ovaries from ducks with high and low egg production |
|
| Relations |
| BioSample |
SAMN06131565 |
| SRA |
SRX2414825 |
