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Sample GSM315781 Query DataSets for GSM315781
Status Public on Mar 31, 2010
Title HPV16-E6 10A_E6 (B)
Sample type RNA
Source name 10A_E6
Organism Homo sapiens
Characteristics SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16-E6
Treatment protocol Cells were cultured at 39 C for three weeks prior to 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 Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.
Label Cy3
Label protocol 500ng of RNA was linearly amplified and fluorescently labeled with either Cy3-CTP or Cy5-CTP with the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Amstelveen, The Netherlands).
Hybridization protocol 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65C 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 Nov 16, 2011
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 Cy3 signal

Data table
12 1826.334593
13 73.71376707
14 1085.792947
15 52.59245976
16 10605.94175
17 70.4750902
18 162.9472097
19 55868.97675
20 57.56809611

Total number of rows: 45220

Table truncated, full table size 759 Kbytes.

Supplementary file Size Download File type/resource
GSM315781_251485011249_S01_GE2_v5_95_Feb07_1_4.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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