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Sample GSM2094177 Query DataSets for GSM2094177
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
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 0.706162223873136
14qI-1_st 2.40699787892289
14qI-1_x_st 1.44107147032141
14qI-2_st 0.76609006666135
14qI-3_x_st 0.706162223873136
14qI-4_st 0.840500031411241
14qI-4_x_st 0.706162223873136
14qI-5_st 0.706162223873136
14qI-6_st 0.835223199957731
14qI-7_st 0.9388235657414
14qI-8_st 0.654508614771019
14qI-8_x_st 0.579144878087462
14qI-9_x_st 0.423864013831377
14qII-10_st 0.412496264927093
14qII-11_st 0.706162223873136
14qII-12_st 0.884375108628891
14qII-12_x_st 0.733294860576403
14qII-13_st 0.770560066018263
14qII-14_st 1.32356678806389
14qII-14_x_st 0.803545457765436

Total number of rows: 36353

Table truncated, full table size 1183 Kbytes.

Supplementary file Size Download File type/resource
GSM2094177_385_PS_RNA_94_miRNA-4_0_.CEL.gz 778.4 Kb (ftp)(http) CEL
Processed data included within Sample table

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