|
| Status |
Public on Feb 04, 2021 |
| Title |
AF_35W rep1 |
| Sample type |
SRA |
| |
|
| Source name |
abdominal fat_35 weeks
|
| Organism |
Cairina moschata |
| Characteristics |
common name: Muscovy duck
age: 35 weeks
tissue: abdominal fat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
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 |
| |
|
| Description |
2-A1_CCGTCC_L004
AF1_35W_FPKM
|
| Data processing |
Raw data (raw reads) were processed using fastx(version:0.0.13). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using tophat(version:2.0.9).
FPKM value of each gene was calculated using cufflinks(version:2.1.1).
and the read counts of each gene were obtained.
DEGs were identified using the cufflinks Cuffdiff functions FoldChange and Fisher-test.
Genome_build: Anas_platyrhynchos.BGI_duck_1.0
Supplementary_files_format_and_content: FPKM values for each Sample with gene_id @ http://asia.ensembl.org/index.html
|
| |
|
| Submission date |
Feb 04, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Xingyong Chen |
| Organization name |
Anhui Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
130 Changjiangxilu
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
| |
|
| Platform ID |
GPL28113 |
| Series (1) |
| GSE144727 |
Abdominal fat mRNA transcriptome of Muscovy duck |
|
| Relations |
| BioSample |
SAMN13978984 |
| SRA |
SRX7670056 |
