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Sample GSM2071104 Query DataSets for GSM2071104
Status Public on Feb 09, 2017
Title FK18BT3-
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 3
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 3_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 4.45035726
A_25_P00015229 4.549504704
A_25_P00016018 4.479330237
A_25_P00011991 5.751239639
A_25_P00015101 4.462787025
A_25_P00010432 4.643706504
A_25_P00015836 4.857953951
A_25_P00010259 4.491233397
A_25_P00015285 4.517862922
A_25_P00015097 4.495010965
A_25_P00012376 6.353057742
A_25_P00012139 6.82610703
A_25_P00015493 4.50763557
A_25_P00012297 4.44002845
A_25_P00010683 5.870360808
A_25_P00015031 4.472940577
A_25_P00015444 4.502424335
A_25_P00012542 4.471766974
A_25_P00015003 4.552780384
A_25_P00015755 4.53408121

Total number of rows: 3101

Table truncated, full table size 81 Kbytes.




Supplementary file Size Download File type/resource
GSM2071104_US22502676_253118113317_S01_miRNA_107_Sep09_2_3.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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