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Sample GSM853219 Query DataSets for GSM853219
Status Public on Feb 01, 2012
Title HeLa ctl siRNA, biological replicate 1, miRNA
Sample type RNA
Source name HeLa cells, control siRNA
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: cervical adenocarcinoma
treatment: control siRNA
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 control siRNA-transfected HeLa cells, biological replicate #1.
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 8.20323
AFFX-BioB-M_at 8.86006
AFFX-BioB-3_at 8.88482
AFFX-BioC-5_at 9.94164
AFFX-BioC-3_at 8.87999
AFFX-BioDn-5_at 10.6162
AFFX-BioDn-3_at 12.1845
AFFX-CreX-5_at 13.2502
AFFX-CreX-3_at 13.4454
AFFX-r2-Ec-c1-bioB-5_st 1.00641
AFFX-r2-Ec-c1-bioB-M_st 0.585616
AFFX-r2-Ec-c1-bioB-3_st 3.182
AFFX-r2-Ec-c1-bioC-5_st 2.79852
AFFX-r2-Ec-c1-bioC-3_st 0.731577
AFFX-r2-Ec-c1-bioD-5_st 3.4917
AFFX-r2-Ec-c1-bioD-3_st 2.00509
AFFX-r2-P1-c1-cre-5_st 4.07331
AFFX-r2-P1-c1-cre-3_st 2.17451
AFFX-r2-Ec-c2-bioB-5_st 1.11584
AFFX-r2-Ec-c2-bioB-M_st 1.87524

Total number of rows: 7815

Table truncated, full table size 186 Kbytes.

Supplementary file Size Download File type/resource
GSM853219.CEL.gz 149.5 Kb (ftp)(http) CEL
GSM853219.chp.gz 62.1 Kb (ftp)(http) CHP
Processed data included within Sample table

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