|
| Status |
Public on Apr 07, 2016 |
| Title |
Tumor_Fibroblasts_Vehicle_Patient_44 |
| Sample type |
RNA |
| |
|
| Source name |
Colon tumor fibroblasts, vehicle-treated, patient 44
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Vehicle
tissue: Colon tumor fibroblasts
patient: Patient 44
|
| Treatment protocol |
Primary human colon normal and tumor fibroblasts cultured in Fibroblast Growth Medium 2 (Lonza, Basel, Switzerland) were treated with 1,25(OH)2D3 (Sigma-Aldrich, San Louis, MO) or vehicle (ethanol) and incubated for 48 h at 37 ºC in a humidified incubator with 5% CO2.
|
| Growth protocol |
Primary cultures of colon normal and tumor fibroblasts were established following the explant outgrowth technique from fresh surgical specimens of normal colon mucosa and colon primary tumor resected from colorectal cancer patients.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin miRNA extraction kit (Macherey-Nagel, Düren, Germany) following manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 100 ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit following manufacturer's instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.
|
| |
|
| Hybridization protocol |
Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µl. Temperature (ºC): 65. Duration: 17 h.
|
| Scan protocol |
Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. Normexp background subtraction was performed.
|
| Description |
Gene expression profile of colon tumor fibroblast primary culture established from patient 44 and treated with vehicle for 48 h
|
| Data processing |
Quantile normalization was performed using limma package available at Bioconductor
|
| |
|
| Submission date |
Jul 02, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Maria Jesus Larriba |
| E-mail(s) |
[email protected]
|
| Organization name |
Instituto de Investigaciones Biomedicas "Alberto Sols"
|
| Department |
Cancer Biology
|
| Street address |
Arturo Duperier 4
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE70468 |
Vitamin D receptor expression and associated gene signature in tumor stromal fibroblasts predict clinical outcome in colorectal cancer |
|
| Relations |
| Reanalyzed by |
GSE113533 |
