NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM319369 Query DataSets for GSM319369
Status Public on Apr 13, 2009
Title Thyroid_normal1_rep2
Sample type RNA
 
Channel 1
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 555
Label protocol Alexa 555 label protocol
 
Channel 2
Source name normal thyroid tissue
Organism Homo sapiens
Characteristics normal thyroid tissue
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
1 341 110 90 79 null
2 339 107 105 76 null
3 308 99 91 79 null
4 310 98 134 81 null
5 313 101 111 79 null
6 333 103 139 77 null
7 322 103 95 80 null
8 315 118 377 83 null
9 307 96 98 79 null
10 334 103 99 78 null
11 344 112 99 76 null
12 336 109 103 78 null
13 717 117 855 79 2.64451426536568
14 310 97 105 76 null
15 3844 133 539 82 -0.628281607151163
16 511 116 135 80 -0.800157925143357
17 321 104 117 80 null
18 487 123 241 81 -0.00415331831251642
19 309 96 111 77 null
20 321 110 180 82 null

Total number of rows: 4800

Table truncated, full table size 154 Kbytes.




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