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Sample GSM1779987 Query DataSets for GSM1779987
Status Public on Apr 07, 2016
Title Tumor_Fibroblasts_1,25(OH)2D3_Patient_11
Sample type RNA
Source name Colon tumor fibroblasts, 1,25(OH)2D3-treated, patient 11
Organism Homo sapiens
Characteristics treatment: 1,25(OH)2D3
tissue: Colon tumor fibroblasts
patient: Patient 11
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 11 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 13.60280167
A_33_P3246448 8.973627946
A_33_P3318220 6.038780013
A_33_P3236322 6.403817112
A_33_P3319925 6.480832116
A_21_P0000509 12.7421013
A_21_P0000744 9.704062504
A_24_P215804 6.38744665
A_23_P110167 8.796627493
A_33_P3211513 6.86432884
A_23_P103349 6.009486884
A_32_P61480 6.19357651
A_33_P3788124 6.105027478
A_33_P3414202 7.601723747
A_33_P3316686 7.588734083
A_33_P3300975 6.643507147
A_33_P3263061 12.10495932
A_33_P3261373 6.247807277
A_24_P278460 7.808119002
A_21_P0013109 6.175512237

Total number of rows: 50599

Table truncated, full table size 1256 Kbytes.

Supplementary file Size Download File type/resource
GSM1779987_TD_P11_253949436603_S01_GE1_1105_Oct12_B_1_4.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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