GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2094180 Query DataSets for GSM2094180
Status Public on May 05, 2016
Title Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG), rep3
Sample type RNA
Source name Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG), rep3
Organism Homo sapiens
Characteristics tissue: Caco-2 human epithelial colorectal adenocarcinoma cells
treatment: co-culture (LGG)
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 co-culture (LGG)
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
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

Data table header descriptions
VALUE log-scale RMA signal

Data table
14q0_st 0.481337255042417
14qI-1_st 2.14709056157454
14qI-1_x_st 1.32754056987413
14qI-2_st 0.359781792568466
14qI-3_x_st 0.408527976238082
14qI-4_st 0.384388265641416
14qI-4_x_st 0.230617952860788
14qI-5_st 0.611443091957401
14qI-6_st 0.375425492113738
14qI-7_st 0.948800272886724
14qI-8_st 0.606911756011158
14qI-8_x_st 0.575995597272255
14qI-9_x_st 0.432337844593983
14qII-10_st 0.865031924005403
14qII-11_st 0.881637246047298
14qII-12_st 0.771433782866512
14qII-12_x_st 0.75746019244511
14qII-13_st 1.04386188739719
14qII-14_st 1.11592722231872
14qII-14_x_st 0.686342714755631

Total number of rows: 36353

Table truncated, full table size 1182 Kbytes.

Supplementary file Size Download File type/resource
GSM2094180_380_PS_RNA_108_miRNA-4_0_.CEL.gz 768.9 Kb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap