|
| Status |
Public on Feb 28, 2013 |
| Title |
D2957 unexposed control cells after 60 min, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
D2957 unexposed control cells after 60 min, biological rep3
|
| Organism |
Bifidobacterium longum |
| Characteristics |
strain: D2957
|
| Treatment protocol |
Cell treatments for transcriptome studies. Cells were grown to late loge phase at 37oC under anaerobic conditions with pH control at 6.5 after which four 5 ml samples were aseptically harvested into sterile 200 ml centrifuge bottles and immediately suspended in 50 mL pre-warmed 50 mL pre-warmed MP5 media containing 1.25mM H2O2. Cells were harvested for RNA isolation after 5 min (T1) and 60 min (T2). Cells were immediatly suspended in 100 mL of RNAprotect reagent (QIAGEN, Inc., Valencia,, CA) and incubated at room temperature for 10 min then collected by cetrifugation. Control cells were immediatly suspended in 10 mL of RNAprotect and incubated at room temperature for 10 min hen collected by cetrifugation (C1). Cell pellets were stored at -80oC until RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation. Cell pellets were thawed at room temperature, then carefully suspended in 1 ml of lysozyme solution (20 mg/ml in TE buffer) that also contained 20 Units of mutanolysin (Sigma, St. Louis, MO). This mixture was incubated at 37oC for 30 minutes in a shaker incubator at 240 rpm, then total RNA was isolated from each of the cell samples using the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, CA) following procedures recommended by the vendor.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 55oC on a custom Affymetrex Bifidobacteria Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 according to the Affymetrix protocol.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A according to the Affymetrix protocol..
|
| Description |
Gene expression data from D2957 unexposed control cells after 60 min, biological rep3
|
| Data processing |
The data were analyzed with Bioconductor in the open statistical platform R version 2.9.0 using the robust multiarray average (RMA) muti-species method.
|
| |
|
| Submission date |
Feb 27, 2013 |
| Last update date |
Feb 28, 2013 |
| Contact name |
Taylor S Oberg |
| E-mail(s) |
taylor.oberg@aggiemail.usu.edu
|
| Organization name |
Utah State University
|
| Department |
NDFS
|
| Lab |
Broadbent
|
| Street address |
8700 Old Main
|
| City |
Logan |
| State/province |
UT |
| ZIP/Postal code |
84322 |
| Country |
USA |
| |
|
| Platform ID |
GPL16727 |
| Series (1) |
| GSE44709 |
Expression data from Bifidobacterium longum strains exposed to hydrogen peroxide stress |
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