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Sample GSM126884 Query DataSets for GSM126884
Status Public on Sep 09, 2006
Title AM209
Sample type genomic
 
Channel 1
Source name primary mucosal melanoma
Organism Homo sapiens
Characteristics BRAF & NRAS wt
Extracted molecule genomic DNA
Extraction protocol paraffin embedded formalin fixed tumor
Label CY3
 
Channel 2
Source name reference DNA
Organism Homo sapiens
Characteristics normal DNA
Extracted molecule genomic DNA
Label CY5
 
 
Description Use Spot files "HA3.1_clonepos_May04.20060811.txt " & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample and refer to the Sample platform GPL2024 for the clone name
Data processing Data processing is described in Curtin et al. NEJM, 2005, (353), 2135-3147. Briefly: We acquired 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images using a custom built CCD camera system and carried out image and data analysis using UCSF SPOT. The arrays contain 2462 clones printed as triplicate spots. Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. No other computational adjustments were applied to the data. We used the SPROC software to automatically filter the data based on quality criteria, average the log2 ratios of the replicate spots, and assign genome position. Only clones for which two or more spots passed quality criteria and for which the standard deviation of the replicates was less than 0.2 were included in the subsequent analysis. Data were normalized to set the median log2 ratio to zero. We used only clones that were mapped on the genome sequence and which did not detect copy number polymorphisms in normal samples. Data from submission GSE2631 and submission GSE4747 were derived from three different versions of arrays termed HumArray1-3. For compatibility, only data from clones represented on all three versions of the BAC Arrays and that stem from clones that conform to the above criteria are presented in this table.
 
Submission date Aug 10, 2006
Last update date Aug 25, 2006
Contact name Boris Bastian
E-mail(s) bastian@cc.ucsf.edu
Phone 415-476-5132
Fax 415-476-8218
URL http://www.cc.ucsf.edu/people/bastian_boris.html
Organization name UCSF Cancer Center
Department Laboratory Medicine
Street address
City San Francisco
State/province CA
ZIP/Postal code 94143-0808
Country USA
 
Platform ID GPL2024
Series (1)
GSE4747 Somatic Activation of KIT in Distinct Subtypes of Melanoma

Data table header descriptions
ID_REF
VALUE aka LOG2RATIO, mean of log base 2 of LINEAR_RATIO of the CY3 (test) signal intensity over the CY5 (reference) signal intensity

Data table
ID_REF VALUE
HumArray2H11_C9 0.15044
HumArray2H10_N30 0.050588
HumArray2H10_B18 0.153232
HumArray2H10_Q30 0.553967
HumArray2H10_T30 0.709739
HumArray2H10_B19 -0.003949
HumArray2H10_W30 0.071256
HumArray2H9_C14 0.104085
HumArray2H9_F14 0.257228
HumArray2H9_I14 -0.266904
HumArray2H9_A23 0.019706
HumArray2H9_L14 -0.143878
HumArray2H9_O14 -0.132145
HumArray2H11_L8 0.400394
HumArray2H9_B4 0.191133
HumArray2H9_U14 0.211594
HumArray2H9_R14 0.207711
HumArray2H9_X14 0.128761
HumArray2H9_C17 0.262536
HumArray2H10_S36 0.232086

Total number of rows: 1949

Table truncated, full table size 48 Kbytes.




Supplementary file Size Download File type/resource
GSM126884_CY3.tif.gz 2.2 Mb (ftp)(http) TIFF
GSM126884_CY5.tif.gz 2.0 Mb (ftp)(http) TIFF
GSM126884_DAPI.tif.gz 2.2 Mb (ftp)(http) TIFF

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