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Sample GSM1636503 Query DataSets for GSM1636503
Status Public on Feb 01, 2016
Sample type RNA
Source name Cell treated with C3/C2
Organism Homo sapiens
Characteristics tissue: colon adenocarcinoma
cell line: HT29
agent: C3/C2
Treatment protocol 6 h treatment combining TRAIL (100 ng/ml + 2 µg/ml anti-Flag M2 antibody) with propionibacterial culture supernatant (SN diluted to 1/2) or a mixture of propionate (30 mM) and acetate (15 mM) (C3/C2, the major metabolites used in the amounts present in the diluted SN).
Growth protocol The HT29 human colon adenocarcinoma cell line was obtained from ATCC (American Type Culture Collection, Rockville, MD, USA) and cultured at 37°C under a humidified atmosphere of 5 % CO2 in DMEM medium (GlutaMAXTM, high glucose, Life Technologies, St Aubin, France) supplemented with 10 % heat inactivated-fetal calf serum (FCS)
Extracted molecule total RNA
Extraction protocol standard RNA extraction protocols (NucleoSpin® RNA II).
Label Cy3
Label protocol To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).
Hybridization protocol The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven
Scan protocol Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).
Description Sample name: 253949410822_2_3
Data processing The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
the signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.
Submission date Mar 18, 2015
Last update date Apr 23, 2018
Contact name Nathalie THERET
Organization name University of Rennes 1
Department INSERM U1085
Street address 2 avenue Pr Leon Bernard
ZIP/Postal code 35043
Country France
Platform ID GPL16699
Series (1)
GSE67033 The probiotic Propionibacterium freudenreichii as a new adjuvant for TRAIL-based therapy in colorectal cancer
Reanalyzed by GSE113533

Data table header descriptions
VALUE normalized signal

Data table
4 127.599965
5 0.102141
6 0.088474
7 0.284636
8 0.151270
9 1378.444095
10 3.146368
11 3.173397
12 140.363848
13 6.258420
14 0.137315
15 0.086492
16 0.086267
17 12.863368
18 10.352530
19 30.210422
20 98.847523
21 0.085135
22 18.147254
23 0.084679

Total number of rows: 58717

Table truncated, full table size 873 Kbytes.

Supplementary file Size Download File type/resource
GSM1636503_253949410822_S01_GE1_107_Sep09_2_3.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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