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Sample GSM156522 Query DataSets for GSM156522
Status Public on Feb 01, 2007
Title HCT116 Dicer -/- #2, mock, 24 hr vs. HCT116 Dicer -/- #2, miR_16, 100 nM, 24 hr
Sample type RNA
 
Channel 1
Source name HCT116 Dicer -/- #2
Organism Homo sapiens
Characteristics HCT116 Dicer -/- #2, mock, 24 hr
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 Dicer -/- #2
Organism Homo sapiens
Characteristics HCT116 Dicer -/- #2, miR_16, 100 nM, 24 hr
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 Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, and Lim L. MCB (2007).
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 17, 2007
Last update date Jan 24, 2007
Contact name Julja Burchard
Organization name Merck & Co., Inc.
Department Computational & Systems Biology
Street address 33 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02176
Country USA
 
Platform ID GPL3991
Series (1)
GSE6838 Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_VALUE Corrected Log10 Ratio of channels (CH2/CH1)

Data table
ID_REF VALUE LOGINTENSITY INTENSITY1 INTENSITY2 PVALUE QUALITY UNF_VALUE
10019475365 -0.0204 -0.9653 0.1184 0.1126 7.2313e-001 1 -0.0204
10019481149 -0.0530 -0.4144 0.4106 0.3647 3.3626e-001 1 -0.0530
10019495284 -0.1151 0.4006 2.8735 2.2029 1.9002e-002 1 -0.1151
10019687586 0.0276 -0.9895 0.1009 0.1079 7.2655e-001 1 0.0276
10019713746 -0.0283 -1.0386 0.0949 0.0896 6.6419e-001 1 -0.0283
10019799479 -0.0108 -1.1498 0.0730 0.0706 9.0353e-001 1 -0.0108
10019809115 -0.0091 -0.6303 0.2372 0.2322 8.7686e-001 1 -0.0091
10019874890 -0.0180 -0.9779 0.1080 0.1039 7.5548e-001 1 -0.0180
10019909307 0.0627 -0.8836 0.1216 0.1405 6.6840e-001 1 0.0627
10019911222 -0.0414 -0.2889 0.5392 0.4902 3.5867e-001 1 -0.0414
10019924807 -0.0518 -1.8392 0.0158 0.0137 8.3277e-001 1 -0.0518
10019927856 -0.0778 -0.0817 0.9067 0.7591 1.3493e-001 1 -0.0778
10019932383 0.0012 -0.4819 0.3295 0.3308 9.8243e-001 1 0.0012
10019948931 -0.0302 -1.3788 0.0427 0.0420 8.1997e-001 1 -0.0302
10019975533 0.0625 -1.5782 0.0249 0.0288 6.3258e-001 1 0.0625
10019977227 0.1001 -0.5899 0.2290 0.2927 3.1974e-001 1 0.1001
10019987588 -0.0165 -0.9812 0.1067 0.1031 8.1445e-001 1 -0.0165
10020008603 -0.0228 -0.8949 0.1310 0.1240 7.0569e-001 1 -0.0228
10020014121 0.0317 -0.2371 0.5582 0.6056 6.5956e-001 1 0.0317
10020044367 -0.0688 -0.6947 0.2194 0.1863 2.7641e-001 1 -0.0688

Total number of rows: 23497

Table truncated, full table size 1443 Kbytes.




Supplementary data files not provided

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