|
| Status |
Public on May 05, 2016 |
| Title |
Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Caco-2 human epithelial colorectal adenocarcinoma cells
treatment: control
|
| Treatment protocol |
Caco-2 human epithelial colorectal adenocarcinoma cells were co-cultured with bacteria (Lactobacillus rhamnosus GG (LGG), and Bacteroides caccae and LGG).
|
| Growth protocol |
Caco-2 human epithelial colorectal adenocarcinoma cells were cultured in the HuMiX device.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracts were prepared using the Affymetrix WT PLUS Reagent Kit (Affymetrix). RNA quality and integratiy was checked using a a NanoDrop ND-100 spectrophotometer (Thermo Scientific) and the 2100 Agilent Bioanalyzer (Agilent). For gene expression analysis, 100 ng of total RNA were used in conjunction with the Affymetrix standard protocol for Human Transcriptome Arrays 2.0 (Affymetrix Inc.). For the miRNAs analysis, 1µg of total RNA was analyzed using the FlashTag Biotin HSR RNA labeling kit for the Affymetrix Genechips miRNA 4.0 microarrays (Affymetrix Inc.).
|
| Label |
biotin
|
| Label protocol |
The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA was used for fragmentation and labeling.
|
| |
|
| Hybridization protocol |
The cDNA was hybridized onto Affymetrix Human Gene 2.0 ST Arrays and the Affymetrix GeneChip Hybridization, Wash and Stain Kit was used to hybridize and wash the cartridges. Control Oligonucleotide B2 and 20X Eukaryotic Hybridization Controls were added to the hybridization cocktail containing the labeled sample and injected into the cartridge. The Incubation lasted 16 hr at 45°C with a rotation at 60 rpm. Then, the Fluidics Station 450/250 was used to wash and stain the Affymetrix GeneChip Human Gene 2.0 ST probe arrays.
|
| Scan protocol |
Whole Transcript (WT) Expression Arrays (P/N 703174 Rev. 2) were scanned with a GCS3000 Scanner (Affymetrix) for images and intensities.
|
| Description |
miRNA expression data from Caco-2 human epithelial colorectal adenocarcinoma cells, anaerobic control
|
| Data processing |
The data was processed using R/bioconductor and RMA with default parameters.
|
| |
|
| Submission date |
Mar 18, 2016 |
| Last update date |
May 06, 2016 |
| Contact name |
Enrico Glaab |
| E-mail(s) |
enrico.glaab@uni.lu
|
| Organization name |
University of Luxembourg
|
| Street address |
6, avenue du Swing
|
| City |
Belvaux |
| State/province |
Capellen |
| ZIP/Postal code |
L-4367 |
| Country |
Luxembourg |
| |
|
| Platform ID |
GPL19117 |
| Series (1) |
| GSE79383 |
A microfluidics-based in vitro model of the gastrointestinal human-microbe interface |
|
