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Sample GSM1162286 Query DataSets for GSM1162286
Status Public on Dec 31, 2014
Title colonic mucosal biopsy from pancolitis 19
Sample type RNA
 
Source name Colonic mucosal biopsy from patient with pancolitis
Organism Homo sapiens
Characteristics tissue: Colonic mucosal biopsy from the left side of the colon
disease state: pancolitis
Extracted molecule total RNA
Extraction protocol RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol. Integrity (only samples with a RNA integrity number above 7 were included) and purity were verified with an Agilent Bioanalyzer (Palo Alto, CA, USA).
Label Biotin
Label protocol In accordance with the Affymetrix protocol and the one-cycle eukaryotic target labelling assay, biotin-labelled cRNA was produced
 
Hybridization protocol The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin, and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied.
Scan protocol The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn and scanned with a GeneArray scanner at the excitation wavelength of 488 nm. The amount of light emitted at 570 nm was proportional to the bound target at each location on the probe array.
Data processing By employing the robust multi-array analysis procedure with quantile normalization implemented in the Affymetrix library for the R statistical environment, a single log2 scale expression measure for each probe set was attained from the low level data files (CEL files). Principal component analysis (PCA) was used in order to reduce data complexity. This was performed with the R package pcaGoPromoter, The Hotelling T2 test, which is the multivariate counterpart of a Student’s t-test, was conducted on the two-component PCA model. In brief the scores for each sample were applied to a multiple linear regression model using a dummy variable to encode the classes (left-sided colitis, pancolitis, and dysplasia, respectively). The calculations were performed in R. Dysplasia was tested against pancolitis and left-sided colitis, respectively.
 
Submission date Jun 13, 2013
Last update date Dec 31, 2014
Contact name Jacob Tveiten Bjerrum
E-mail(s) bjerrum.jacob@gmail.com
Phone +45 38681059
Organization name Herlev Hospital
Department Department of Gastroenterology, Medical Section
Street address Herlev Ringvej 75
City Herlev
ZIP/Postal code 2730
Country Denmark
 
Platform ID GPL570
Series (1)
GSE47908 Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 10.7807502995231
1053_at 8.26593379656243
117_at 6.26726601924052
121_at 8.51698952206076
1255_g_at 3.52847916469857
1294_at 8.82444584357292
1316_at 4.7907012981762
1320_at 5.05711102987593
1405_i_at 8.12917770730967
1431_at 4.02179805494258
1438_at 7.76550643135383
1487_at 9.27397007240582
1494_f_at 5.81349239759113
1552256_a_at 8.54118883776445
1552257_a_at 9.96556989378841
1552258_at 4.77764621504631
1552261_at 4.99111748611149
1552263_at 7.34975995755054
1552264_a_at 8.58768363454031
1552266_at 3.76835100488356

Total number of rows: 54675

Table truncated, full table size 1479 Kbytes.




Supplementary file Size Download File type/resource
GSM1162286_Pan_19.CEL.gz 8.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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