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Sample GSM815128 Query DataSets for GSM815128
Status Public on Oct 01, 2012
Title HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 2
Sample type RNA
 
Source name Primary human keratinocytes were cultured from newborn foreskin.
Organism Homo sapiens
Characteristics treatment: Conditioned medium from planktonic S. aureus cultures spiked with DMSO during exponential phase growth.
cell type: Human Foreskin Keratinocytes were isolated at the University of Washington.
Treatment protocol After growing HaCaT cells to confluence, cells were treated for 4 hours at 37C, 5% CO2.
Growth protocol HaCaT keratinocytes were cultured in 6 well plates using EpiLife growth medium supplemented with human keratinocyte growth supplement. Cells were maintained at 37C in a humidified, 5% CO2 atmosphere.
Extracted molecule total RNA
Extraction protocol After treatment, the medium was removed and RNA was isolated using an RNeasy minikit following the manufacturer’s instructions for adherent cells. Extracted RNA was then ethanol precipitated.
Label biotin
Label protocol Total RNA (500ng) was reverse transcribed, and amplified and biotin-labeled via in vitro transcription using the MessageAmp Premier kit
 
Hybridization protocol Labeled and fragmented cRNA was hybridized for 16 hr at 45C to the Affymetrix Human Genome U133A 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using an Affymetrix 7G scanner and GCOS version 1.4.
Description PCM_-_b
Data processing Microarray data were analyzed using FlexArray version 1.6. The Affymetrix CEL files were imported and normalized using GC-RMA.
Matrix files include scaled MAS5 (linked to the Series record) and GC-RMA (contained in the data table below) normalized (log2) values.
 
Submission date Oct 12, 2011
Last update date Oct 01, 2012
Contact name Kate McInnerney
E-mail(s) kmcinnerney@montana.edu
Phone 406-994-5666
Fax 406-994-4926
URL http://cores.montana.edu
Organization name Montana State University
Department Microbiology
Lab Functional Genomics Facility
Street address 109 Lewis Hall
City Bozeman
State/province MT
ZIP/Postal code 59717
Country USA
 
Platform ID GPL571
Series (1)
GSE32920 Phevalin (aureusimine B) production by Staphylococcus aureus biofilm and impacts on human keratinocyte gene expression

Data table header descriptions
ID_REF
VALUE GC-RMA log2 normalized signal intensity

Data table
ID_REF VALUE
212296_at 11.54247921
221368_at 2.010596389
205530_at 4.452361599
217147_s_at 1.707792142
213290_at 2.313876314
209861_s_at 11.20924379
221784_at 2.285993588
217682_at 3.048791863
218090_s_at 9.406639191
212219_at 7.668439006
31846_at 8.91245037
200868_s_at 7.711920539
36612_at 7.18861074
209909_s_at 3.127276151
213746_s_at 11.22733656
219555_s_at 9.80189144
219495_s_at 3.419969608
204522_at 5.185484904
217725_x_at 9.943534928
217675_at 1.783753739

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM815128.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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