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Sample GSM624068 Query DataSets for GSM624068
Status Public on Jan 01, 2011
Title BT15329
Sample type RNA
 
Source name chuR mutant bacteria from C57BL/6 mouse cecum fed simple sugar diet
Organism Bacteroides thetaiotaomicron
Characteristics strain: VPI-5482
genotype: chuR mutant
isolation source: cecum of C57BL/6 mouse fed simple sugar diet
Treatment protocol Total RNA was extracted directly from cecal contents that contained only wild-type or mutant B. thetaiotaomicron.
Extracted molecule total RNA
Extraction protocol Phenol/chloroform bead-beating on cecal contents, Qiagen RNAEasy extraction, Ambicon DNAEasy treatment; Final Qiagen RNAEasy cleanup.
Label biotin
Label protocol Biotin-UDP end labeling.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on custom Affymetrix GeneChip GPL11169. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date Nov 16, 2010
Last update date Jan 01, 2011
Contact name Eric Charles Martens
E-mail(s) emartens@umich.edu
Phone 734-647-5800
Organization name University of Michigan Medical School
Department Dept. of Microbiology and Immunology
Street address 1150 West Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL11169
Series (1)
GSE25415 Transcription analysis of wild-type and chuR Bacteroides thetaiotaomicron genes in the mouse cecum

Data table header descriptions
ID_REF
VALUE Linear, normalized to 500 in Affymetrix MAS5.0
Detection Indicates if the transcript was present (P), absent (A), or marginal (M)

Data table
ID_REF VALUE Detection
AFFX-BioB-5_at 31.14484 A
AFFX-BioB-M_at 386.4455 P
AFFX-BioB-3_at 34.98167 A
AFFX-BioC-5_at 76.97598 A
AFFX-BioC-3_at 96.54748 A
AFFX-BioDn-5_at 232.0604 A
AFFX-BioDn-3_at 143.6712 A
AFFX-CreX-5_at 12.24794 A
AFFX-CreX-3_at 20.13865 A
AFFX-DapX-5_at 7878.603 P
AFFX-DapX-M_at 7337.537 P
AFFX-DapX-3_at 4508.122 P
AFFX-LysX-5_at 603.3901 P
AFFX-LysX-M_at 533.5021 P
AFFX-LysX-3_at 444.4471 P
AFFX-PheX-5_at 1580.141 P
AFFX-PheX-M_at 1686.888 P
AFFX-PheX-3_at 724.2845 P
AFFX-ThrX-5_at 1931.927 P
AFFX-ThrX-M_at 1371.051 P

Total number of rows: 22993

Table truncated, full table size 493 Kbytes.




Supplementary file Size Download File type/resource
GSM624068.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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