Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]

Affymetrix GeneChip Human Genome U133A 2.0 [HG-U133A_2]

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processedData

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The objective of the experiment was to compare changes in the transcriptome induced by direct X-irradiation of cells, using the human K562 erythroleukemic, Me45 melanoma and HCT116 colon cancer cell lines. The transcript levels of K542 and Me45 RNA samples were measured using Affymetrix HG-U133A microarrays and for HCT116 with HGU 133A 2.0 in time points 1, 12, 24 h after irradiation and compared to the levels of RNA from control cells. Experiments were repeated twice for Me45 and K562 cells.

CELL_LINE

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GENETIC_MODIFICATION

IRRADIATE

TIME

Transcription profiling of human cell lines K562, Me45 and HCT116 with or without p53 knock-out to study the effect of ionizing radiation

The objective of the experiment was to compare changes in the transcriptome induced by direct X-irradiation of cells, using the human K562 erythroleukemic, Me45 melanoma and HCT116 colon cancer cell lines. The transcript levels of K542 and Me45 RNA samples were measured using Affymetrix HG-U133A microarrays and for HCT116 with HGU 133A 2.0 in time points 1, 12, 24 h after irradiation and compared to the levels of RNA from control cells. Experiments were repeated twice for Me45 and K562 cells.


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MTAB-13067

P-MTAB-13068

P-MTAB-13069

P-MTAB-13070

P-MTAB-13356

The results from all raw Affymetrix HGU-133A and HGU-133A_2 microarrays obtained in this series of hybridizations were normalized using RMAExpress program (Me45+K562 and HCT116 separately due to different microarray type). To assign a single value of hybridization signal to each gene, we tested the RMA-normalized signals from different probe sets representing the same gene for the presence of outliers according to the Dixon procedure as described in (Jaksik et al, 2009), probesets were removed if they were classified as outliers in at least 90% samples. Remaining probesets were averaged for each individual gene. Further analysis was performed on average values from two repeated samples.

Transcription profiling of human cell lines K562, Me45 and HCT116 with or without p53 knock-out to study the effect of ionizing radiation

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