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| Status |
Public on Aug 27, 2015 |
| Title |
XHl |
| Sample type |
SRA |
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| Source name |
Breast muscle
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| Organism |
Gallus gallus |
| Characteristics |
strain: Xing Hua Chicken
phenotype: slow-growing
age: 7 Weeks
group: low body weight
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| Treatment protocol |
Breast muscle tissues of the 3 individuals were collected immediately after euthanized, snap frozen in liq nitrogen, then stored at -80°C until RNA extraction.
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| Growth protocol |
All broilers were reared in cages with a 24-h photoperiod for the first 2 d of age and then changed to a 16-h photoperiod. They were fed with free access to water and fedad libitum with 16.5% CP and 2, 800 kcal of ME/kg. According to the body weight (BW) records at 7 weeks, three female birds from each of the two-tail groups of WRR and XH were selected, and then four groups including WRRh (the group of Recessive White Rock with high body weight), WRRl (the group of Recessive White Rock with low body weight), XHh (the group of Xinhua Chickens with high body weight) and XHl (the group of Xinhua Chickens with low body weight) were generated. The averages of body weight values were 1,064.0 ± 11.1, 695.0 ± 24.4, 305.8 ± 23.3, and 207.6 ± 11.1 g for WRRh, WRRl, XHh, and XHl group, respectively.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each breast muscle using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions. The quality and concentration of all twelve RNA samples were determined by 1.5% agarose gel electrophoresis and absorbance at A260/280 ratio, and then divided to four mixed RNA pools for WRRh, WRRl, XHh, and XHl.
mRNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gallus gallus whole genome using TopHat.
To estimate the expression of each gene, the total number of reads mapped to its unigenes were calculated and normalized with FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Gallus_gallus.Galgal4.73
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| Submission date |
Aug 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Biao |
| E-mail(s) |
biaochen123@hotmail.com
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| Phone |
+86 18931507508
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| Organization name |
Jiangxi Agricultural University
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| Department |
College of animal science and technology
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| Street address |
Zhimin main street 1101#
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| City |
Nanchang |
| State/province |
Jiang Xi |
| ZIP/Postal code |
330045 |
| Country |
China |
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| Platform ID |
GPL16133 |
| Series (1) |
| GSE72424 |
A Genome-wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth |
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| Relations |
| BioSample |
SAMN04013384 |
| SRA |
SRX1165470 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1862267_XHl.xls.gz |
1.5 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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