|
| Status |
Public on Aug 26, 2016 |
| Title |
colorectal adenoma, patient 16 (exon) |
| Sample type |
RNA |
| |
|
| Source name |
colorectal adenoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: adenoma
localisation: sigmoid colon
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Colon or rectum biopsy samples were obtained after surgical removal and informed patient consent. The tissue fragments were stored in RNAlater (Ambion, France). DNA and total RNA were extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (AgilentTM). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
colorectal adenoma, patient 16
colorectal adenoma biopsy
|
| Data processing |
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Sep 04, 2013 |
| Last update date |
Aug 26, 2016 |
| Contact name |
Pierre de la Grange |
| E-mail(s) |
[email protected]
|
| Organization name |
GenoSplice technology
|
| Department |
Paris Biotech Santé
|
| Street address |
29, rue du Faubourg Saint-Jacques
|
| City |
Paris |
| ZIP/Postal code |
75014 |
| Country |
France |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE50592 |
Expression data from colorectal biopsy samples - adenomas or normal mucosae |
|
| Relations |
| Alternative to |
GSM1224335 (gene level analysis) |
