|
| Status |
Public on Mar 16, 2019 |
| Title |
HN_liver_3 |
| Sample type |
SRA |
| |
|
| Source name |
liver of broiler fed with high-fat diet
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Xinghua
age: 8-weeks-old
diet: high-fat diet
tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Livers and abdominal fats were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
liver RNA_repeat 3
|
| Data processing |
BGI SOAPnuke software used for trimming and filtering.
Sequenced reads were mapped to gga5 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Gene expression analysis step 1: sequenced reads were then mapped to gga5 whole genome using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
Gene expression analysis step 2: Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using RSEM v1.2.12.
Genome_build: gga5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 15, 2019 |
| Last update date |
Mar 16, 2019 |
| Contact name |
Wen Luo |
| E-mail(s) |
luowen729@scau.edu.cn
|
| Organization name |
South China Agricultural University
|
| Street address |
Wushan
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL24996 |
| Series (1) |
| GSE128340 |
Differentially expressed genes in livers and abdominal fats between normal- and high-fat diet-fed chickens |
|
| Relations |
| BioSample |
SAMN11130391 |
| SRA |
SRX5524949 |
