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Sample GSM210974 Query DataSets for GSM210974
Status Public on Jan 01, 2008
Title Undifferentiated Dicer -/- (27H) ES cell line transfected with siRL replicate_3
Sample type RNA
 
Source name Embryonic stem cell transfected with siRL
Organism Mus musculus
Characteristics Undifferentiated Dicer -/- ES cell line, passage 22, transfected with siRNA against Renilla luciferase
Extracted molecule total RNA
Extraction protocol Absolutely RNA Miniprep Kit (Stratagene)
Label biotinylated cRNA
Label protocol cRNA was produced by in vitro transcription (IVT) by T7 RNA polymerase, using the Affymetrix IVT kit as per manufacturer’s instructions.
 
Hybridization protocol 20 µg of biotinylated cRNA was fragmented by heating in the presence of Mg2+ (as per Affymetrix’s instructions) and 15 µg of fragmented cRNA was hybridized to Mouse MOE430 v2.0 GeneChips™
Scan protocol standard Affymetrix procedures
Description ES cells deficient of Dicer_transfected with siRNA agains Renilla luciferase
_date of analysis 01072007
Data processing Quality control and background normalization were performed using Refiner from Genedata AG (Basel, Switzerland). All arrays were condensed together using the GC-RMA algorithm with quantile normalization composed of 100 bins using Genedata’s Refiner application. Per chip normalization was performed by scaling the median of the genes called present (detection p-value < 0.04) to a value of 500. Per chip normalized data are referred to as “raw” expression values.
 
Submission date Jul 17, 2007
Last update date Aug 28, 2018
Contact name Lasse Sinkkonen
E-mail(s) lasse.sinkkonen@fmi.ch
Organization name Friedrich Miescher Institute
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL1261
Series (1)
GSE8503 mRNA expression analysis of undifferentiated Dicer -/- (27H10) embryonic stem cells after miRNA transfection
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE normalized signal intensity
ABS_CALL Whether transcript is concidered present or absent
DETECTION P-VALUE significance of detection

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 626.583 P 6.02111e-05
AFFX-BioB-M_at 885.572 P 4.42873e-05
AFFX-BioB-3_at 553.826 P 4.42873e-05
AFFX-BioC-5_at 1520.05 P 4.42873e-05
AFFX-BioC-3_at 1776.86 P 4.42873e-05
AFFX-BioDn-5_at 5070.39 P 4.42873e-05
AFFX-BioDn-3_at 7550.23 P 4.42873e-05
AFFX-CreX-5_at 18387.5 P 5.16732e-05
AFFX-CreX-3_at 22289.2 P 4.42873e-05
AFFX-DapX-5_at 6.89364 A 0.354453
AFFX-DapX-M_at 2.9106 A 0.953518
AFFX-DapX-3_at 17.7702 A 0.659339
AFFX-LysX-5_at 2.96174 A 0.559359
AFFX-LysX-M_at 1.75809 A 0.993129
AFFX-LysX-3_at 19.8987 P 0.0464816
AFFX-PheX-5_at 0.54093 A 0.963443
AFFX-PheX-M_at 3.12523 A 0.937071
AFFX-PheX-3_at 15.2629 A 0.361399
AFFX-ThrX-5_at 13.8826 A 0.574038
AFFX-ThrX-M_at 1.1014 A 0.945817

Total number of rows: 45101

Table truncated, full table size 1382 Kbytes.




Supplementary file Size Download File type/resource
GSM210974.CEL.gz 3.1 Mb (ftp)(http) CEL
GSM210974.CHP.gz 255.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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