|
| Status |
Public on Aug 18, 2021 |
| Title |
ileum flora in broiler at 14 d, control group, rep5 |
| Sample type |
SRA |
| |
|
| Source name |
ileum flora of broiler
|
| Organism |
Gallus gallus |
| Characteristics |
age: 14 d
tissue: ileum
agent: control
|
| Treatment protocol |
Chicks in the SP, SPH, and SPM groups were orally treated with a 0.5 ml S. pullorum solution at 5 days of age, while chicks in the control (CTL) group received the same amount of sterilized PBS at the same age.At 14 and 21 days of age, one chick from each replicate was randomly selected to be weighed and slaughtered by jugular exsanguination after a 12-h fasting period. The ileum samples were collected to analyze the gene expression.
|
| Growth protocol |
A total of 360 one-day-old broilers were selected and randomly divided into four groups with six replicates: the negative control group (CTL), S. pullorum-infected group (SP), and the S. pullorum-infected group supplemented with 300 mg/kg honokiol (SPH) or magnolol (SPM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CTL_5
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCg6a
Supplementary_files_format_and_content: txt file include FPKM values for each Sample…
Supplementary_files_format_and_content: text file include novel genes…
|
| |
|
| Submission date |
Jan 05, 2021 |
| Last update date |
Aug 18, 2021 |
| Contact name |
fang chen |
| E-mail(s) |
zhhchenfang0730@hotmail.com
|
| Phone |
86-13476267589
|
| Organization name |
Hubei Academy of Agricultural Sciences
|
| Street address |
No1, Nanhu Road
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430064 |
| Country |
China |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE164260 |
Next Generation Sequencing of ileum in broiler infected with S. pullorum |
|
| Relations |
| BioSample |
SAMN17215359 |
| SRA |
SRX9782618 |
