|
| Status |
Public on Oct 24, 2021 |
| Title |
KA194A0381-H006S94X_L001 |
| Sample type |
SRA |
| |
|
| Source name |
Breast muscle
|
| Organism |
Anas platyrhynchos |
| Characteristics |
age: 42 day after birth
duck type: duck with the low breast muscle ratios (LB)
|
| Growth protocol |
All ducks were farmed under the same breeding conditions. Food and water were provided ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Breast muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 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 |
| |
|
| Description |
F2 duck population
|
| Data processing |
To obtain high-quality clean reads, the reads were filtered using fastp (version 0.18.0). Reads were removed if they contained adapters, more than 10% unknown nucleotides (N), or more than 50% low-quality (Q-value ≤ 20) bases.
The clean reads were mapped to the duck reference genome using HISAT2.2.4.
The mapped reads of each sample were assembled using StringTie v1.3.1
For each transcription region, the fragments per kilobase of transcript per million mapped reads (FPKM) were analyzed to quantify expression abundance.
RNA differential expression analysis was performed using DESeq2 software.
Genome_build: Anas platyrhynchos (mallard) CAU__Wild1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Oct 10, 2021 |
| Last update date |
Oct 24, 2021 |
| Contact name |
Zhixiu Wang |
| E-mail(s) |
ZHIXIUQAU111@126.com
|
| Phone |
+8615652503739
|
| Organization name |
China Agricultural University
|
| Street address |
No. 2 Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL22591 |
| Series (1) |
| GSE185612 |
Identification of Genes Related to Growth Traits from Transcriptome Profiles of Duck Breast Muscle Tissue |
|
| Relations |
| BioSample |
SAMN22204991 |
| SRA |
SRX12566008 |
