|
| Status |
Public on Dec 31, 2014 |
| Title |
colonics mucosal biopsy from dysplasia 3 |
| Sample type |
RNA |
| |
|
| Source name |
Colonic mucosal biopsy from patient with ulcerative colitis-associated dysplasia
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colonic mucosal biopsy from the left side of the colon
disease state: ulcerative colitis-associated dysplasia
|
| 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 |
|
