|
| Status |
Public on Feb 01, 2016 |
| Title |
SN REPLICATE 4 |
| Sample type |
RNA |
| |
|
| Source name |
Cell treated with SN
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon adenocarcinoma
cell line: HT29
agent: 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: 253949410823_1_4
|
| 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 |
