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Sample GSM2071105 Query DataSets for GSM2071105
Status Public on Feb 09, 2017
Title FK18BT4-
Sample type RNA
 
Source name primary human foreskin keratinocytes transfected with HPV18
Organism Homo sapiens
Characteristics cell type: HPV18-transfected human foreskin keratinocytes_line B
transformation stage: anchorage independent
timepoint: timepoint 4
treatment: no treatment
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 HPV18-transfected human foreskin keratinocytes_line B_timepoint 4_untreated
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 4.418356232
A_25_P00015229 4.505320206
A_25_P00016018 4.409122031
A_25_P00011991 5.988707853
A_25_P00015101 4.478968285
A_25_P00010432 4.693141889
A_25_P00015836 4.682355733
A_25_P00010259 4.445083432
A_25_P00015285 4.519517634
A_25_P00015097 4.431693271
A_25_P00012376 6.276134831
A_25_P00012139 6.862880247
A_25_P00015493 4.540121479
A_25_P00012297 4.379332584
A_25_P00010683 5.770409954
A_25_P00015031 4.531244806
A_25_P00015444 4.478228745
A_25_P00012542 4.502686027
A_25_P00015003 4.527113073
A_25_P00015755 4.632018267

Total number of rows: 3101

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM2071105_US22502676_253118114752_S01_miRNA_107_Sep09_2_1.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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