NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1089202 Query DataSets for GSM1089202
Status Public on Feb 28, 2013
Title D2957 unexposed control cells after 60 min, biological rep1
Sample type RNA
 
Source name D2957 unexposed control cells after 60 min, biological rep1
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 rep1
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

Data table header descriptions
ID_REF
VALUE RMA-MS processed log2 signal intensity

Data table
ID_REF VALUE
BL0001_RBLO00001_at 10.357539
BL0001_RBLO00001_s_at 12.408416
BL0002_RBLO00002_at 13.502575
BL0003_RBLO00003_s_at 11.280895
BL0004_RBLO00004_at 11.325864
BL0005_RBLO00005_s_at 11.958481
BL0006_RBLO00006_at 11.966191
BL0007_RBLO00007_at 11.517538
BL0008_RBLO00008_at 11.680869
BL0009_RBLO00009_at 11.824981
BL0010_RBLO00010_at 12.51151
BL0011_RBLO00011_at 11.405887
BL0012_RBLO00012_at 11.301565
BL0013_RBLO00013_at 11.60442
BL0014_RBLO00014_s_at 11.661837
BL0015_RBLO00015_at 10.083776
BL0015_RBLO00015_s_at 11.578252
BL0016_RBLO00016_at 12.061503
BL0017_RBLO00017_at 12.043345
BL0018_RBLO00018_at 12.271775

Total number of rows: 3114

Table truncated, full table size 93 Kbytes.




Supplementary file Size Download File type/resource
GSM1089202_D2957_C2_R1.CEL.gz 516.5 Kb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap