NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM156557 Query DataSets for GSM156557
Status Public on Feb 01, 2007
Title HCT116 Dicer -/- #2, mock, 24 hr vs. HCT116 Dicer -/- #2, hsa-let-7c, 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, hsa-let-7c, 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 0.0123 -0.9065 0.1228 0.1261 8.3763e-001 1 0.0123
10019481149 0.0115 -0.3433 0.4484 0.4611 8.1291e-001 1 0.0115
10019495284 0.0133 0.3567 2.2437 2.3125 7.6803e-001 1 0.0133
10019687586 -0.0262 -1.0327 0.0956 0.0900 6.0363e-001 1 -0.0262
10019713746 0.0272 -1.1224 0.0734 0.0782 6.7450e-001 1 0.0272
10019799479 0.0358 -1.2336 0.0563 0.0611 5.0834e-001 1 0.0358
10019809115 -0.0101 -0.7272 0.1897 0.1855 8.7317e-001 1 -0.0101
10019874890 -0.0048 -1.2412 0.0577 0.0573 9.4210e-001 1 -0.0048
10019909307 0.0438 -0.9891 0.0998 0.1169 7.1515e-001 1 0.0438
10019911222 -0.0241 -0.5313 0.3058 0.2893 5.9151e-001 1 -0.0241
10019924807 -0.0067 -1.3734 0.0431 0.0425 9.2921e-001 1 -0.0067
10019927856 -0.0985 -0.0997 0.8948 0.7096 9.2991e-002 1 -0.0985
10019932383 -0.0040 -0.6065 0.2486 0.2464 9.3705e-001 1 -0.0040
10019948931 0.0457 -1.6796 0.0199 0.0222 6.9469e-001 1 0.0457
10019975533 0.0017 -1.6719 0.0211 0.0216 9.8847e-001 1 0.0017
10019977227 -0.0418 -0.7425 0.1925 0.1749 7.2246e-001 1 -0.0418
10019987588 -0.0077 -1.1037 0.0818 0.0810 9.2169e-001 1 -0.0077
10020008603 0.0038 -1.0645 0.0942 0.0949 9.5018e-001 1 0.0038
10020014121 0.0390 -0.2413 0.5489 0.6095 6.8542e-001 1 0.0390
10020044367 -0.0410 -0.7380 0.1929 0.1754 3.7418e-001 1 -0.0410

Total number of rows: 23603

Table truncated, full table size 1447 Kbytes.




Supplementary data files not provided
Raw data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap