|
| Status |
Public on Dec 20, 2018 |
| Title |
Control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
control_hypothalamus
|
| Organism |
Sus scrofa |
| Characteristics |
strain: Duroc x Landrace x Large White
age: post natal day 45
treated with: saline (0.9% NaCl) solution
tissue: hypothalamus
|
| Treatment protocol |
Twelve piglets were randomly assigned to 1 of 2 groups using a randomized complete block design: infused 10 mL solution of saline (0.9% NaCl) through T-cannula in the distal ileum as the control group or infused 10 mL saline with the antibiotic combination (ampicillin, 150 mg/kg/day; gentamicin, 4 mg/kg/day; and metronidazole, 30 mg/kg/day) as the antibiotic group.
|
| Growth protocol |
Piglets were housed individually in metabolic cages under a comfortable environment with temperature maintained at 26 ± 2 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hypothalamus was 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 HiSeq 4000 |
| |
|
| Description |
pigs fitted with T cannula in distal ileum
|
| Data processing |
Illumina Casava1.7 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: susScr3
Supplementary_files_format_and_content: RPKM expression data of differential genes
|
| |
|
| Submission date |
Apr 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kan Gao |
| E-mail(s) |
kevingogh911@hotmail.com
|
| Phone |
86 15088629137
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
No.1 Weigang Road
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE97738 |
Distal ileal antibiotic infusion affects the expressions of neurotransmitters in the hypothalamus of piglets |
|
| Relations |
| BioSample |
SAMN06718724 |
| SRA |
SRX2734522 |
