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Sample GSM2094176 Query DataSets for GSM2094176
Status Public on May 05, 2016
Title Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep2
Sample type RNA
 
Source name Caco-2 human epithelial colorectal adenocarcinoma cells, miRNA, anaerobic control, rep2
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

Data table header descriptions
ID_REF
VALUE log-scale RMA signal

Data table
ID_REF VALUE
14q0_st 0.686342714755631
14qI-1_st 1.82835557208512
14qI-1_x_st 1.02398989150471
14qI-2_st 0.893593605071311
14qI-3_x_st 0.449685703445131
14qI-4_st 0.612419740983476
14qI-4_x_st 0.462092600953176
14qI-5_st 0.338207385657725
14qI-6_st 0.48942406491104
14qI-7_st 1.44298084671495
14qI-8_st 0.808246726908297
14qI-8_x_st 0.7698439148355
14qI-9_x_st 0.735295817914859
14qII-10_st 0.607358064726781
14qII-11_st 0.914199756391819
14qII-12_st 0.868746621470611
14qII-12_x_st 0.75746019244511
14qII-13_st 0.777284664454505
14qII-14_st 1.18837516114598
14qII-14_x_st 0.768630959959236

Total number of rows: 36353

Table truncated, full table size 1181 Kbytes.




Supplementary file Size Download File type/resource
GSM2094176_379_PS_RNA_88_miRNA-4_0_.CEL.gz 760.7 Kb (ftp)(http) CEL
Processed data included within Sample table

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