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Sample GSM1779988 Query DataSets for GSM1779988
Status Public on Apr 07, 2016
Title Tumor_Fibroblasts_1,25(OH)2D3_Patient_16
Sample type RNA
Source name Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 16
Organism Homo sapiens
Characteristics treatment: 1,25(OH)2D3
tissue: Colon tumor fibroblasts
patient: Patient 16
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 16 and treated with 1,25(OH)2D3 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
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
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized log2 intensity

Data table
A_23_P117082 13.78260822
A_33_P3246448 11.97716903
A_33_P3318220 6.036034372
A_33_P3236322 6.174442556
A_33_P3319925 6.216276538
A_21_P0000509 12.4751754
A_21_P0000744 9.299970274
A_24_P215804 6.260632381
A_23_P110167 10.70952459
A_33_P3211513 7.038457604
A_23_P103349 6.174442556
A_32_P61480 6.10052918
A_33_P3788124 6.065568202
A_33_P3414202 6.776819637
A_33_P3316686 7.181000526
A_33_P3300975 8.748291421
A_33_P3263061 12.55231592
A_33_P3261373 6.216276538
A_24_P278460 8.417524445
A_21_P0013109 6.136128866

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM1779988_TD_P16_253949436603_S01_GE1_1105_Oct12_B_1_1.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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