NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM319410 Query DataSets for GSM319410
Status Public on Apr 13, 2009
Title Colon_normal1_rep1
Sample type RNA
 
Channel 1
Source name normal colon tissue
Organism Homo sapiens
Characteristics normal colon tissue
Extracted molecule total RNA
Extraction protocol Trizol
Label Alexa 555
Label protocol Alexa 555 label protocol
 
Channel 2
Source name reference RNA pool
Organism Homo sapiens
Characteristics RNA pool of 15 distinct cell lines
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM00637
Extracted molecule total RNA
Extraction protocol Trizol
Label Alexa 647
Label protocol Alexa 647 label protocol
 
 
Hybridization protocol Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 2 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deionized formamide 40% / Temperature:42 / Time:12-24h / Touch Down: 70, 55, 50, 42
Washing - Round 1 - Solution: 2X SSC 0,1% SDS / Temperature:42 / Time:4 min / Washing Number: 1
Washing - Round 2 - Solution: 0,1 SSC 0,1% SSC / Temperature:42 / Time:4 min / Washing Number: 1
Washing - Round 3 - Solution: 0,1X SSC / Temperature:42 / Time:rinse / Washing Number: 3
Washing - Round 4 - Solution: 0,1X SSC / Temperature:42 / Time:4 min / Washing Number: 4
Washing - Round 5 - Solution: 0,1X SSC / Temperature:42 / Time:rinse / Washing Number: 5
Scan protocol Slides were scanned on a confocal laser scanner (ScannArray Express, Perkin Elmer), using identical parameters for all slides and data was extracted with ScanArray Express software (Perkin Elmer). Glass Slides were scanned at different photomultiplier tube (pmt) gains, being 70% and 60% for the channels 1 (Alexa Fluor 555) and 2 (Alexa Fluor 647), respectively.
Description Reference RNA: Daudi (Burkitt's lymphoma), DLD-1 (colorectal adenocarcinoma), DU 145 (prostate carcinoma), FaDu (pharinx squamous cell carcinoma), GM-637 (fibroblast), H-146 (small cell lung carcinoma), HT-1080 (fibrosarcoma), HB4a (normal mammary luminal epithelium), HEK (human embryonic kidney), Jurkat (acute T cell leukemia), Saos-2 (osteosarcoma), SK-BR-3 (breast adenocarcinoma), SK-MEL-28 (melanoma), T24 (bladder transitional cell carcinoma), T98G (glioblastoma multiforme).
Data processing After subtracting local background, data was normalized by Lowess (R Project) and dye swaps were reversed during normalization.
 
Submission date Sep 10, 2008
Last update date May 13, 2009
Contact name Barbara Pereira Mello
E-mail(s) bmello@lbhc.hcancer.org.br
Phone 55-11-2189-5000-1134
Organization name Hospital A. C. Camargo
Department Centro de Pesquisa
Lab LBHC
Street address R. Prof. Antonio Prudente, 211
City Sao Paulo
State/province SP
ZIP/Postal code 01509-900
Country Brazil
 
Platform ID GPL7262
Series (1)
GSE12737 No-match ORESTES explored as tumor markers

Data table header descriptions
ID_REF this column should correspond to the ID column of the reference platform
IntCH1 Channel 1 Intensity
BkgCH1 BackGround Channel 1
IntCH2 Channel 2 Intensity
BkgCH2 BackGround Channel 2
VALUE value normalized by Lowess representing test/reference RNA pool

Data table
ID_REF IntCH1 BkgCH1 IntCH2 BkgCH2 VALUE
1 344 114 170 82 null
2 354 119 192 82 null
3 313 106 301 79 null
4 328 111 204 81 null
5 299 105 331 81 null
6 246 110 355 84 null
7 329 107 304 85 null
8 327 117 385 84 null
9 338 102 235 80 null
10 310 121 361 88 null
11 363 121 181 84 null
12 338 118 258 80 null
13 416 127 1082 81 1.60536711644492
14 328 105 311 81 null
15 347 149 4408 93 -0.624708485351877
16 207 123 664 84 -0.727794611005045
17 328 115 344 82 null
18 183 130 619 88 -0.382277987441149
19 344 112 238 83 null
20 283 123 389 92 null

Total number of rows: 4800

Table truncated, full table size 144 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap