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Sample GSM575314 Query DataSets for GSM575314
Status Public on Aug 29, 2011
Title v-ras-Ha transformed keratinocytes without IL1ra, rep3
Sample type RNA
 
Source name v-ras-Ha transformed keratinocytes with PBS treatment
Organism Mus musculus
Characteristics genotype: wild type
developmental stage: newborn
tissue: epidermis
cell type: v-ras-Ha-transduced keratinocytes
treatment: PBS
Treatment protocol Primary mouse keratinocytes and hair follicle buds were isolated from newborn epidermis from wild type mice. Keratinocytes were adenovirus infected for 30 min with serum-free medium with a multiplicity of infection of 10 viral particles/cell and 4 ug/ml of Polybrene (Sigma) to enhance uptake. Five hours post v-rasHa-transduction, interleukin-1-receptor antagonist, Anakinra (Amgen, Inc, Thousand Oaks, CA), was added to the keratinocytes cultures at a final concentration of 5 ug/ml . Cultures were kept for an extra 3 days but IL-1Ra was replaced after 2 days. Thereafter, RNA from IL1R antagonist- or PBS-treated cultures was prepared.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested from cultured v-rasHa-transduced keratinocytes in the presence of PBS or Anakinra. Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions. RNA was purified using the RNAeasy Min-elute (Qiagen) RNA isolation kit. Total RNA samples were quantitated by UV spectrophotometry (OD260/280). Quality of the total RNA was assessed by using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Alexa-555
Label protocol First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer.
 
Hybridization protocol cRNA was fragmented to uniform size and hybridized to Agilent Whole Genome 4x44K arrays.
Scan protocol Slides were washed and scanned on an Agilent G2565 Microarray Scanner.
Description Control_9
Data processing The gProcessSignal of Agilent Feature Extraction data was normalized using a global median-based method and filtered by the Agilent feature extraction flag “gIswellAboveBG” to eliminate bad probes with signals consistently lower than background across the samples. All of these procedures were done with customized R scripts (www.r-project.org).
 
Submission date Aug 05, 2010
Last update date Aug 29, 2011
Contact name Rosalba Salcedo
E-mail(s) lmirosi@mail.ncifcrf.gov
Phone 301-846-6274
Fax 301-846-6641
Organization name SAIC-NCI
Street address 1050 Boyles Street, Bldg. 567
City Frederick
State/province MD
ZIP/Postal code 21701
Country USA
 
Platform ID GPL4134
Series (1)
GSE22777 Autocrine IL-1α mediates NF-κB activation by oncogenic ras in keratinocytes

Data table header descriptions
ID_REF
VALUE Global median-based normalized intensity value

Data table
ID_REF VALUE
12 3.135
13 3.727
14 1.992
15 1.992
16 6.983
18 3.804
19 1.989
20 4.686
21 4.172
22 10.185
23 11.515
24 8.624
25 3.377
26 4.118
27 9.742
28 12.771
29 8.149
30 1.981
31 1.981
32 2.829

Total number of rows: 43379

Table truncated, full table size 508 Kbytes.




Supplementary file Size Download File type/resource
GSM575314.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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