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Sample GSM2094181 Query DataSets for GSM2094181
Status Public on May 05, 2016
Title Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG+B.caccae), rep1
Sample type RNA
 
Source name Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic co-culture (LGG+B.caccae), rep1
Organism Homo sapiens
Characteristics tissue: Caco-2 human epithelial colorectal adenocarcinoma cells
treatment: co-culture (LGG+B.caccae)
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+B.caccae)
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

Data table header descriptions
ID_REF
VALUE log-scale RMA signal

Data table
ID_REF VALUE
14q0_st 0.580501335383821
14qI-1_st 2.24926942210362
14qI-1_x_st 1.44490374152322
14qI-2_st 0.33700961808957
14qI-3_x_st 0.357642051745748
14qI-4_st 0.823840587664334
14qI-4_x_st 0.706162223873136
14qI-5_st 0.984093700932295
14qI-6_st 0.531860052200292
14qI-7_st 1.31147417471629
14qI-8_st 1.0676946259522
14qI-8_x_st 1.03181725248235
14qI-9_x_st 0.273407712891716
14qII-10_st 0.381125210876936
14qII-11_st 0.538611211695682
14qII-12_st 0.774501467816417
14qII-12_x_st 0.352773247374547
14qII-13_st 0.85480149706083
14qII-14_st 1.10754972940398
14qII-14_x_st 1.10123607947567

Total number of rows: 36353

Table truncated, full table size 1183 Kbytes.




Supplementary file Size Download File type/resource
GSM2094181_388_PS_RNA_12_miRNA-4_0_.CEL.gz 802.1 Kb (ftp)(http) CEL
Processed data included within Sample table

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