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Sample GSM161587 Query DataSets for GSM161587
Status Public on Apr 23, 2007
Title Mouse ileum with L.innocua(inlA)_B_5558
Sample type RNA
 
Source name Fabpi-hEcad transgenic C57BL/6J mouse ileum- 72h monoassociation with L.innocua(inlA)_B_5558
Organism Mus musculus
Characteristics 12-15 week old, male, gnotobiotic Fabpi-hEcad C57BL/6J transgenic mice that express hEcad in small intestinal enterocytes under the control of nucleotides -1178 to +28 of the rat Fabpi gene_ileum (pool of 4 animals)_72h monoassociation with L.innocua(inlA)_B_5558
Extracted molecule total RNA
Extraction protocol RNA was purified from ileum of each mouse [Midi RNeasy kit (Qiagen) with on-column DNase digestion]. Equivalent amounts of RNA from mice in each treatment group (n=4/experiment) were pooled and two biotinylated cRNA targets (40 ug/replicate) were independently prepared from each sample.
Label biotin
Label protocol In vitro transcription (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) was performed on cRNA derived from 40ug total RNA followed by standard fragmentation. For detailed protocol see http://pathimm.wustl.edu/~mgacore/protocols.htm
 
Hybridization protocol Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
Scan protocol Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
Description ileum (pool of 4 animals)_72h monoassociation with L.innocua(inlA)_B_5558
Data processing MAS5; scaling = 500
 
Submission date Feb 10, 2007
Last update date Apr 23, 2007
Contact name Justin L. Sonnenburg
E-mail(s) [email protected]
Phone 314-362-5443
URL http://gordonlab.wustl.edu/metaview/bt
Organization name Washington University
Department Center for Genome Sciences
Lab Jeffrey I. Gordon
Street address 4444 Forest Park
City Saint Louis
State/province MO
ZIP/Postal code 63108
Country USA
 
Platform ID GPL81
Series (1)
GSE7013 Gnotobiotic mouse ileum; Listeria infection series

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
100001_at 68.5 A 0.660442
100002_at 128.3 A 0.697453
100003_at 251.5 A 0.162935
100004_at 691 P 0.011447
100005_at 3079.1 P 0.000562
100006_at 167.6 A 0.234557
100007_at 2521.7 P 0.001354
100009_r_at 187.7 P 0.02786
100010_at 4115.4 P 0.000219
100011_at 9249.7 P 0.000219
100012_at 2289.1 A 0.138765
100013_at 2848.8 P 0.000673
100014_at 359.3 P 0.005643
100015_at 1381.5 P 0.017001
100016_at 295.7 A 0.175989
100017_at 479.2 A 0.089405
100018_at 1137.9 A 0.098054
100019_at 107.4 A 0.910595
100020_at 2153.5 P 0.004863
100021_at 35.3 A 0.892699

Total number of rows: 12488

Table truncated, full table size 327 Kbytes.




Supplementary file Size Download File type/resource
GSM161587.CEL.gz 2.8 Mb (ftp)(http) CEL
GSM161587.EXP.gz 316 b (ftp)(http) EXP

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