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Sample GSM1585918 Query DataSets for GSM1585918
Status Public on Mar 31, 2015
Title S9_HLA_1
Sample type RNA
 
Source name cell line S9
Organism Homo sapiens
Characteristics origin: human bronchium
cell line: S9
condition: alpha-toxin treatment
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the TRIzol reagent (Invitrogen). RNA was purified using the RNA Clean-Up and Concentration Micro Kit (Norgen) and concentrations were measured using a ND-1000 spectrophotometer (Thermo Fisher Scientific Inc). RNA integrity was validated by means of the lab-on-chip capillary electrophoresis technology (Bioanalyzer 2100, Agilent Technologies). Only RNA samples with an RNA integrity number (RIN)>9.5 [34], 260/280 nm≥1.8, 260/230 nm≥1.9 were used for microarray analyses.
Label biotin
Label protocol For each sample, 200 ng of total RNA was reverse transcribed into cDNA, amplified, and in vitro transcribed to cRNA. Sense-strand cDNA was generated from 10 µg of purified cRNA using random primers, followed by fragmentation and labelling using 5.5 µg of purified sense-strand DNA.
 
Hybridization protocol Biotinylated sense-strand DNA was then hybridized onto the Affymetrix GeneChip Human Gene 1.0 ST arrays for 16 h. Arrays were washed and stained using the Fluidics Station 450.
Scan protocol Scanning was performed by GeneChip Scanner 3000 7G (Affymetrix); raw CEL files were generated using the GCOS software. Quality assessment of all hybridizations was carried out by inspecting scan images and by reviewing external and endogenous controls using the Expression Console software (Affymetrix).
Description Gene expression data from S9 cells treated with alpha-toxin.
Data processing Data analysis was carried out using Rosetta Resolver system for gene expression data analysis (Rosetta Bio software). In brief, the raw signals of the gene-specific probes were summarized using the Robust Multi-array Average algorithm and data transformation for array comparability was achieved by performing quantile normalization. Genes exhibiting significantly different expression on the RNA level were identified using the following cut-off criteria: one-way analysis of variance with subsequent Benjamini and Hochberg false discovery rate multiple-testing correction on pair-wise comparisons (ANOVA, p≤0.05), signal correction statistics (Ratio Builder, p≤0.05) and fold-change≥1.5-fold. Probe-set transformation into genes was performed by using the Rosetta Resolver transformation tool based on the Entrez Genes/Unigenes search engine (NCBI).
processed_data.txt: Columns A to C: Gene Identification; Columns D to J: Summarized Intensity signals; Column L & O: Fold Change, Column M,N and P, Q: p-value and post hoc p-value, respectively
 
Submission date Jan 15, 2015
Last update date Mar 31, 2015
Contact name Joerg Mostertz
E-mail(s) mostertz@uni-greifswald.de
Organization name Greifswald University
Department Competence Center Functional Genomics
Lab Pathoproteomics
Street address F.-L.-Jahnstr 15
City Greifswald
ZIP/Postal code 17489
Country Germany
 
Platform ID GPL6244
Series (1)
GSE65018 The epithelial cell transcriptome after alpha-toxin treatment

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
7896736 212
7896738 17
7896740 21
7896742 264
7896744 45
7896746 1298
7896748 237
7896750 79
7896752 2120
7896754 137
7896756 112
7896759 213
7896761 239
7896779 332
7896798 314
7896817 479
7896822 1071
7896859 183
7896861 38
7896863 114

Total number of rows: 29085

Table truncated, full table size 335 Kbytes.




Supplementary file Size Download File type/resource
GSM1585918_S9_HLA_1.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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