|
| Status |
Public on Nov 27, 2018 |
| Title |
Resistance Female 17 |
| Sample type |
genomic |
| |
|
| Source name |
Streptococcus Suis Serotype 2 Resistance Female mouse
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Survival under infection
|
| Treatment protocol |
The SS2 inoculum for experimental infection was adjusted to a concentration of 1×108 CFU/mL. Seventy male and seventy female F2 mice were injected i.p. with a 1 mL inoculum per mouse. F2 mice surviving for fewer than 3 days following infection were regarded as susceptible (22 males and 22 females), while those surviving for more than 15 days were regarded as resistant (23 males and 21 females).
|
| Growth protocol |
A/J and C57BL/6 mice were purchased from Model Animal Research Center of Nanjing University (Nanjing, China). A/J male mice were mated with C57BL/6 female mice to generate an F1 population. For generation of F2 progeny, F1 male mice were mated with inbred F1 female mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blood samples were collected aseptically from susceptible and resistant F2 mice. Genomic DNA was extracted from blood using TIANamp Genomic DNA Kit,
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Zhe Ma |
| E-mail(s) |
mazhe320@gmail.com
|
| Phone |
13585200623
|
| Organization name |
nanjing agricultural university
|
| Street address |
Tonwei Road No.1
|
| City |
Nanjing |
| State/province |
JS |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL13147 |
| Series (2) |
| GSE122963 |
Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis (SNP) |
| GSE122966 |
Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis |
|
