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Sample GSM2071114 Query DataSets for GSM2071114
Status Public on Feb 09, 2017
Title FK16AT5+
Sample type RNA
 
Source name primary human foreskin keratinocytes transfected with HPV16
Organism Homo sapiens
Characteristics cell type: HPV16-transfected human foreskin keratinocytes_line A
transformation stage: anchorage independent
timepoint: timepoint 5
treatment: 5000 nM 5-aza-2’-deoxycytidine (DAC)
Treatment protocol cells were treated with 5000 nM 5-aza-2’-deoxycytidine (DAC; Sigma-Aldrich, Zwijndrecht, The Netherlands) dissolved in PBS for 5 days. DAC was added to the cells every day.
Growth protocol Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines was described previously (Steenbergen et al, Oncogene 1996).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol Reagent according to the manufacturer’s instructions (Life Technologies).
Label Cy3
Label protocol According to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
 
Hybridization protocol According to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
Scan protocol protocol name: miRNA_107_Sep09. Scanning is done according to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
Description HPV16-transfected human foreskin keratinocytes_line A_timepoint 5_DAC treated
Data processing Probes corresponding to human miRNAs were selected and replicates weakly correlating to all other replicates of the same probe were removed. Data was normalized per treatment group using the robust quantile method (Bolstad et al, Bioinformatics 2003) and transformed using the variance stabilizing transformation (Huber, Bioinformatics 2002). The obtained values were averaged per probe for further analysis.
 
Submission date Feb 24, 2016
Last update date Feb 09, 2017
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 GPL15159
Series (2)
GSE78278 Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [miR-Agilent]
GSE78279 Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence

Data table header descriptions
ID_REF
VALUE Normalized signal intensities

Data table
ID_REF VALUE
A_25_P00015543 4.479244932
A_25_P00015229 4.566642819
A_25_P00016018 4.503503036
A_25_P00011991 5.873704507
A_25_P00015101 4.542872077
A_25_P00010432 4.631107588
A_25_P00015836 4.921142421
A_25_P00010259 4.517540438
A_25_P00015285 4.570879521
A_25_P00015097 4.544313838
A_25_P00012376 6.925607019
A_25_P00012139 7.175235833
A_25_P00015493 4.620437891
A_25_P00012297 4.356024901
A_25_P00010683 5.813383695
A_25_P00015031 4.584862369
A_25_P00015444 4.621959626
A_25_P00012542 4.948341836
A_25_P00015003 4.531767861
A_25_P00015755 4.634572096

Total number of rows: 3101

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM2071114_US22502676_253118113323_S01_miRNA_107_Sep09_2_1.txt.gz 8.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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