|
Status |
Public on Mar 16, 2019 |
Title |
NN_liver_2 |
Sample type |
SRA |
|
|
Source name |
liver of broiler fed with normal diet
|
Organism |
Gallus gallus |
Characteristics |
strain: Xinghua age: 8-weeks-old diet: normal 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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
|
|
Description |
liver RNA_repeat 2
|
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
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|
|
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 |
SAMN11130389 |
SRA |
SRX5524951 |