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Sample GSM315762 Query DataSets for GSM315762
Status Public on Mar 31, 2010
Title p53shRNA 10A_SH (A)
Sample type RNA
Source name 10A_SH
Organism Homo sapiens
Characteristics SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53shRNA
Treatment protocol Cells were cultured at 39 °C for three weeks prior RNA extraction.
Growth protocol SV40 ts-LTA-hTERT oral keratinocytes were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recombinant EGF (2.5 ug/500 ml medium)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Trizol (Invitrogen, breda, The Netherlands), according to the manufacturer's instructions. Total RNA was further analyzed on the bioanalyzer (Agilent) and only RIN values of 8 or above were included.
Label Cy5
Label protocol 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
Hybridization protocol 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 °C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.
Description NA
Data processing Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. After normalization, the separate intensity channels were extracted from the ratio measurements
Submission date Aug 27, 2008
Last update date Mar 31, 2010
Contact name Daoud Sie
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
Platform ID GPL4133
Series (1)
GSE12553 Gene expression profiles following TP53 downregulation

Data table header descriptions
VALUE Normalized Intensity Cy5 signal

Data table
12 1915.29445
13 65.38694998
14 824.7485786
15 59.55745308
16 13438.59041
17 58.10696476
18 246.2298792
19 61871.03545
20 60.29607234

Total number of rows: 45220

Table truncated, full table size 759 Kbytes.

Supplementary file Size Download File type/resource
GSM315762_251485011249_S01_GE2_v5_95_Feb07_1_1.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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