|
| Status |
Public on Apr 02, 2010 |
| Title |
Expression_AA-Liver_AG |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Gallus gallus |
| Characteristics |
breed: avian broiler
|
| Treatment protocol |
Two 7-day-old chickens were utilized in this experiment, one red jungle fowl and one avian broiler. The chickens were fed with the same diet and sacrificed according to local standards of animal welfare issues. Liver and muscle tissues taken from each animal were flash frozen in liquid nitrogen and then stored at -80°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The mRNAs were isolated and reverse transcribed into double-stranded cDNA on magnetic beads which were covered with oligo d(T), the cDNA was digested with NlaIII and ligated to Illumina specific adapter containing a recognition site of MmeI. Following Mme1 digestion, a second Illumina adapter, containing a 2 bp degenerate 3’ overhang was ligated. Then tags that were close to the 3’ terminus of the mRNA were enriched by an 15 cycles PCR. The PCR products were run on a 6% TBE-PAGE gel and the ~85bp DNA band was excised and purified for cluster generation and sequencing analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
RNA sequencing
|
| Data processing |
The sequences obtained by RNA-seq were mapped onto the refSeq database. Unmapped and redundantly mapped sequences were removed from the dataset. Sequences uniquely mapped to refseq genes were used for subsequent analysis. All libraries were normalized to 1M sequences according to clean sequences (sequences without undefined nucleotides and excluding sequences that were sequenced only once or contained adaptor sequences).
|
| |
|
| Submission date |
Apr 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
qinghe li |
| E-mail(s) |
lqhcau@163.com
|
| Organization name |
China Agricultural university
|
| Street address |
no2, yuanmingyuan west road
|
| City |
beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL10223 |
| Series (2) |
| GSE21169 |
Examination of whole genome gene expression profiles of two chicken breeds |
| GSE21170 |
Genome-wide Differential DNA Methylation in the Wild and Domestic Chicken |
|
| Relations |
| SRA |
SRX018727 |
| BioSample |
SAMN00010872 |
