|
| Status |
Public on Jun 21, 2019 |
| Title |
OTA [O2 ] |
| Sample type |
SRA |
| |
|
| Source name |
primary hepatocytes
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: primary hepatocytes
agent: OTA treated
|
| Treatment protocol |
Hepatocytes were prepared using a collagenase digestion method
|
| Growth protocol |
Eighteen-day embryonated specific-pathogen-free (SPF) chicken eggs were purchased from the Institute of Animal Science, Guangdong Academy of Agricultural Sciences (Guangzhou, China).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chicken embryo primary hepatocytes were re-suspended in Williams E medium
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The index of the reference genome was built using Bowtie v2.2.3
Paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
The read numbers mapping to each gene were calculated by HTSeq v0.6.1
FPKM of each gene was calculated based on the length of the gene and the reads count mapped to that gene
Differential expression analysis was performed using the DESeq R package
Genome_build: GenBank Assembly ID GCA_000002315.3
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample
|
| |
|
| Submission date |
Apr 09, 2018 |
| Last update date |
Jun 21, 2019 |
| Contact name |
Yu Sun |
| E-mail(s) |
sunyu@scau.edu.cn
|
| Organization name |
South China Agricultural University
|
| Street address |
Tianhe Qu, Wushan
|
| City |
Guangzhou |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL24517 |
| Series (1) |
| GSE112862 |
RNAseq data for chicken liver cells under mycotoxin treatment |
|
| Relations |
| BioSample |
SAMN08897294 |
