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Sample GSM1636519 Query DataSets for GSM1636519
Status Public on Feb 01, 2016
Title T+SN REPLICATE 3
Sample type RNA
 
Source name Cell treated with TRAIL + SN
Organism Homo sapiens
Characteristics tissue: colon adenocarcinoma
cell line: HT29
agent: TRAIL + SN
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: 253949410824_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
City RENNES
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
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
4 134.644266
5 0.295797
6 0.137896
7 0.137627
8 0.397239
9 854.850690
10 1.957618
11 0.136454
12 125.316714
13 15.775945
14 0.135485
15 0.135149
16 0.134804
17 19.326227
18 11.157240
19 33.519585
20 109.689521
21 0.133008
22 30.356344
23 0.132262

Total number of rows: 58717

Table truncated, full table size 874 Kbytes.




Supplementary file Size Download File type/resource
GSM1636519_253949410824_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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