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

Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes

rawData

scan

processedDataMatrix

The experiment was designed to generate a time series for epithelial model during development. Each time point had 3 replicates. The data set contained 5 time points over 10 days. They are day0, day3, day5,day7,day10.

time

Transcription profiling time series of human epithelial cells during development

The experiment was designed to generate a time series for epithelial model during development. Each time point had 3 replicates. The data set contained 5 time points over 10 days. They are day0, day3, day5,day7,day10.


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

The EpiDerm™ 200 skin equivalent cultures were prepared at MatTek Corporation following their standard protocol. Normal human epidermal keratinocytes (NHEK) were initially grown on plastic in monolayer culture before harvest by trypsinization. These freshly harvested cells (time 0 days) were then seeded onto collagen-coated microporous membrane inserts (Millicell CM, Millipore Corp., Bedford, MA) in serum-free, low-calcium growth medium and cultured submerged for one day at 37ºC in a 5% CO2 incubator.  The day after seeding, the medium was changed to high calcium to promote differentiation.  After two additional days of submerged culture in high calcium medium the inserts were raised to the air-liquid interface by removal of the medium from the apical compartment (time 3 days). Air-liquid interface culture continued for a total of seven days (time 5, 7, 10 days) in order to produce the fully differentiated epidermal equivalents.  The culture medium was serum-free throughout the process.

In the experiment, the whole data set was normalized by set of normalization methods. The data were normalized in affy package in R. I chose 4 modules in this package, background correct (Mas 5.0), normalization method (quantiles), PM correct method (pmonly) and summary method (avgdiff). The Mas 5.0 and the avgdiff are two standard methods applied in Affiymetrix system. The quantile method is a fast method which provides each chip the same empirical distribution.

Transcription profiling time series of human epithelial cells during development

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