GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM815129 Query DataSets for GSM815129
Status Public on Oct 01, 2012
Title HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 3
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_-_c
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 11.47669719
221368_at 2.072094972
205530_at 4.489443221
217147_s_at 1.595763521
213290_at 2.305553811
209861_s_at 10.86753141
221784_at 2.343132133
217682_at 3.032447855
218090_s_at 8.304174021
212219_at 7.693461149
31846_at 8.708860624
200868_s_at 7.969273299
36612_at 7.211153233
209909_s_at 2.359741047
213746_s_at 11.4430438
219555_s_at 9.800927725
219495_s_at 3.276219564
204522_at 5.156966914
217725_x_at 10.03724091
217675_at 1.687127059

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM815129.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap