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Sample GSM315768 Query DataSets for GSM315768
Status Public on Mar 31, 2010
Title HPV16_E6 19A_E6 (A)
Sample type RNA
 
Source name 19A_E6
Organism Homo sapiens
Characteristics SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16_E6
Treatment protocol Cells were cultured at 39C 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, 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 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 Mar 31, 2010
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
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
ID_REF
VALUE Normalized Intensity Cy5 signal

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12 1602.102341
13 187.5988181
14 559.0362144
15 55.58142353
16 24302.2325
17 48.80145935
18 206.8457462
19 70238.50648
20 57.95369997

Total number of rows: 45220

Table truncated, full table size 759 Kbytes.




Supplementary file Size Download File type/resource
GSM315768_251485011586_S01_GE2_v5_95_Feb07_1_3.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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