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Sample GSM853224 Query DataSets for GSM853224
Status Public on Feb 01, 2012
Title HeLa Ars2 siRNA #3, miRNA
Sample type RNA
Source name HeLa cells, Ars2 siRNA-3
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: cervical adenocarcinoma
treatment: Ars2 siRNA-3
Treatment protocol HeLa cells were transfected with siRNAs using RNAiMAX (Invitrogen) according to the manufacturer's recommendations.
Growth protocol HeLa cells were grown in DMEM containing 10% FCS.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol reagent according to the manufacturer's instructions.
Label biotin
Label protocol 2ug of total RNA was labeled using the microRNA FlashTag Biotin HSR kit following the manufacturer's instructions.
Hybridization protocol Biotin-labeled microRNAs were hybridized according to the manufacturer's recommendations.
Scan protocol An Affymetrix GCS3000 laser scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
Description miRNA expression data from Ars2 siRNA #3-transfected HeLa cells.
Data processing Affymetrix miRNA QCTool was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Submission date Dec 22, 2011
Last update date Feb 01, 2012
Contact name Scott H Olejniczak
Phone 716-912-2723
Organization name Memorial Sloan Kettering Cancer Center
Street address 417 E68th St
City New York
State/province NY
ZIP/Postal code 10044
Country USA
Platform ID GPL8786
Series (2)
GSE34680 Effects of Ars2 or DGCR8 siRNA on microRNA expression
GSE34681 Effects of Ars2 or DGCR8 siRNA on gene and microRNA expression

Data table header descriptions
VALUE RMA-calculated signal intensity

Data table
AFFX-BioB-5_at 8.63797
AFFX-BioB-M_at 9.43683
AFFX-BioB-3_at 9.52114
AFFX-BioC-5_at 10.3185
AFFX-BioC-3_at 9.42809
AFFX-BioDn-5_at 10.9257
AFFX-BioDn-3_at 12.4028
AFFX-CreX-5_at 13.3608
AFFX-CreX-3_at 13.4354
AFFX-r2-Ec-c1-bioB-5_st 0.825073
AFFX-r2-Ec-c1-bioB-M_st 0.920361
AFFX-r2-Ec-c1-bioB-3_st 3.511
AFFX-r2-Ec-c1-bioC-5_st 3.13181
AFFX-r2-Ec-c1-bioC-3_st 0.892003
AFFX-r2-Ec-c1-bioD-5_st 3.80547
AFFX-r2-Ec-c1-bioD-3_st 2.19149
AFFX-r2-P1-c1-cre-5_st 4.36061
AFFX-r2-P1-c1-cre-3_st 2.40634
AFFX-r2-Ec-c2-bioB-5_st 0.784001
AFFX-r2-Ec-c2-bioB-M_st 1.93441

Total number of rows: 7815

Table truncated, full table size 186 Kbytes.

Supplementary file Size Download File type/resource
GSM853224.CEL.gz 143.5 Kb (ftp)(http) CEL
GSM853224.chp.gz 62.0 Kb (ftp)(http) CHP
Processed data included within Sample table

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