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Sample GSM815127 Query DataSets for GSM815127
Status Public on Oct 01, 2012
Title HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 1
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_-_a
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
Phone 406-994-5666
Fax 406-994-4926
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
VALUE GC-RMA log2 normalized signal intensity

Data table
212296_at 11.47531201
221368_at 2.077861031
205530_at 4.12175499
217147_s_at 1.358444604
213290_at 2.273369939
209861_s_at 11.29105614
221784_at 2.132786638
217682_at 2.702348253
218090_s_at 9.635077044
212219_at 7.117824553
31846_at 8.819807755
200868_s_at 7.478563047
36612_at 7.559144132
209909_s_at 2.519267886
213746_s_at 11.15663314
219555_s_at 9.846558754
219495_s_at 3.169760897
204522_at 5.010015246
217725_x_at 10.20838085
217675_at 1.691770452

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM815127.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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