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Sample GSM739085 Query DataSets for GSM739085
Status Public on Jan 31, 2016
Title INA6 cells using MAT (IL-6 restimulation) ChipD
Sample type RNA
 
Source name Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours
Organism Homo sapiens
Characteristics cell line: INA6
tumor: multiple myeloma
treatment: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.
 
Hybridization protocol Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.
Scan protocol Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.
Description Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Expression data was processed with MAT.
Data processing Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 1e-5 which yielded the best results from the set of tested parameter values.
 
Submission date Jun 08, 2011
Last update date Jan 31, 2016
Contact name Kristin Reiche
E-mail(s) kristin.reiche@izi.fraunhofer.de
Organization name Fraunhofer Institute for Cell Therapy and Immunology
Department Diagnostics
Street address Perlickstr. 1
City Leipzig
ZIP/Postal code 04103
Country Germany
 
Platform ID GPL6159
Series (2)
GSE29824 Expression analysis of INA6 cells after IL-6 restimulation using MAT
GSE29826 Differential expression analysis of INA6 cells using MAT

Supplementary file Size Download File type/resource
GSM739085.CEL.gz 19.6 Mb (ftp)(http) CEL
Processed data are available on Series record

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