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Sample GSM157111 Query DataSets for GSM157111
Status Public on Apr 10, 2007
Title HCT116 Mock 24h b vs. HCT116 MAPK14-esiRNA1 10nM 24h b2
Sample type RNA
 
Channel 1
Source name HCT116
Organism Homo sapiens
Characteristics HCT116_Mock_24h_b
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy spin columns with DNAse treatment
Label Cy3
Label protocol custom automated version of the aminoallyl MessageAmp II kit from Ambion.
 
Channel 2
Source name HCT116
Organism Homo sapiens
Characteristics HCT116_MAPK14-esiRNA1_10nM_24h_b2
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy spin columns with DNAse treatment
Label Cy5
Label protocol custom automated version of the aminoallyl MessageAmp II kit from Ambion.
 
 
Hybridization protocol Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
Scan protocol Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.
Description R. Kittler, V. Surendranath, A.-K. Heninger, M. Slabicki, M. Theis, G. Putz, K. Franke, A. Caldareli, H. Grabner, K. Kozak, J. Wagner, E. Rees, B. Korn, C. Sachse, B. Sonnichsen, J. Guo, J. Schelter, J. Burchard, P.S. Linsley, A.L. Jackson, B. Habermann, and F. Buchholz, Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies, 2007, Nature Methods
Data processing Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
 
Submission date Jan 19, 2007
Last update date Apr 10, 2007
Contact name Aimee Jackson
Organization name Regulus Therapeutics
Street address 1896 Rutherford Rd
City Carlsbad
State/province CA
ZIP/Postal code 92008
Country USA
 
Platform ID GPL4372
Series (1)
GSE6807 Genome-wide resources of endoribonucleotide-prepared short interfering RNAs for specific loss-of-function studies

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE Corrected Log10 Ratio of channels (CH2/CH1)
LOGINTENSITY Corrected average log intensity of channels
INTENSITY1 Cy3 intensity (CH1)
INTENSITY2 Cy5 intensity (CH2)
PVALUE P-value of LogRatio
QUALITY 1 - if good and non control, 0 - otherwise

Data table
ID_REF VALUE LOGINTENSITY INTENSITY1 INTENSITY2 PVALUE QUALITY
10019475365 -0.0191 -1.0927 0.0836 0.0786 8.4042e-001 1
10019481149 0.0297 -0.2692 0.5216 0.5576 5.5935e-001 1
10019495284 0.0355 0.4329 2.6355 2.8524 4.5247e-001 1
10019687586 -0.1358 -1.0513 0.1106 0.0786 1.1907e-001 1
10019713746 -0.0612 -0.8873 0.1424 0.1208 6.0648e-001 1
10019799479 0.0371 -1.0476 0.0861 0.0934 5.7835e-001 1
10019809115 0.0428 -0.7581 0.1704 0.1876 3.8810e-001 1
10019874890 0.0031 -0.9783 0.1071 0.1077 9.6580e-001 1
10019903058 0.0360 -2.2357 0.0110 0.0064 9.6386e-001 1
10019909307 0.1810 -1.0350 0.0753 0.1133 2.2476e-002 1
10019911222 -0.1738 -0.3017 0.6358 0.4231 6.5280e-004 1
10019924807 -0.0586 -1.9020 0.0162 0.0114 8.7897e-001 1
10019927856 -0.0417 -0.0386 1.0727 0.9894 4.2154e-001 1
10019932383 0.0180 -0.3943 0.3994 0.4215 7.5982e-001 1
10019948931 0.0251 -1.3475 0.0448 0.0465 8.3798e-001 1
10019975533 -0.1565 -1.6418 0.0279 0.0194 2.6243e-001 1
10019977224 -0.0380 -0.4314 0.3869 0.3557 5.2926e-001 1
10019977227 -0.0246 -0.6365 0.2383 0.2255 6.7058e-001 1
10019987588 -0.0947 -0.9327 0.1458 0.1135 2.3898e-001 1
10020008603 -0.0159 -0.6101 0.2525 0.2438 7.6058e-001 1

Total number of rows: 39136

Table truncated, full table size 2117 Kbytes.




Supplementary data files not provided

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