Affymetrix GeneChip Chicken Genome Array [Chicken]

Regulation of the DNA Damage Response and Gene Expression by the Dot1L Histone Methyltransferase and the 53Bp1 Tumour Suppressor

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processedData

Effect of abrogation of the histone methyltransferase Dot1L on gene expression in the chicken DT40 model system

GENOTYPE

Transcription profiling by array of chicken wild type and tumor supressor Dot1L knockout lymphoblast cells

Three biological replicates were analysed for each genotype

Effect of abrogation of the histone methyltransferase Dot1L on gene expression in the chicken DT40 model system


Affymetrix:Protocol:Hybridization-Unknown

P-MTAB-14209

Affymetrix .CEL files were imported into GeneSpring GX v7.3 using RMA preprocessing. Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample. Each gene was divided by the median of its measurements in all samples. If the median of the normalized values was below 0.01 then each measurement for that gene was divided by 0.01 if the numerator was above 0.01, otherwise the measurement was thrown out. Median polishing was done, where each chip was normalized to its median and each gene was normalized to its median. These normalizations were repeated until the medians converged. Prior to median polishing, normalized values below 0.01 were replaced with 0.01. 

Transcription profiling by array of chicken wild type and tumor supressor Dot1L knockout lymphoblast cells

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