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Sample GSM143870 Query DataSets for GSM143870
Status Public on Oct 08, 2007
Title 1M-42_2a
Sample type genomic
 
Channel 1
Source name 1M-42_2a
Organism Homo sapiens
Characteristics HCT116+chr3, clone 1M-42
Treatment protocol methotrexate resistant colony derived from clone 1M-42
Extracted molecule genomic DNA
Extraction protocol Cell line DNA was isolated by incubation overnight at 55º C in 3 ml of 1x TE buffer (pH=7.5) supplemented with 0.5 % SDS and 0.1 µg/µl proteinase K, followed by ethanol precipitation after 24 hours.
Label Cy3
Label protocol Genomic DNA (600 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.
 
Channel 2
Source name Genomic DNA (600 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.
Organism Homo sapiens
Characteristics gender: male,
tissue type: blood
Extracted molecule genomic DNA
Extraction protocol Reference genomic DNA was isolated from whole blood of healthy male doner. DNA was prepared using standard methods ie. cell lysis and proteinase K digestion followed by ETOH precipitation. Detailed protocol can be found at http://cancer.ucsf.edu/array/protocols/index.php.
Label Cy5
Label protocol Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5 dCTP in a 50 µl reaction.
 
 
Hybridization protocol Labeled test and reference DNAs together with 100 µg human Cot-1 DNA were hybridized for ~48 hrs at 37º C.
Scan protocol We acquired 16-bit DAPI, Cy3 and Cy5 images using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).
Description Used Spot files "HA3.1_clonepos_May04.20060811.txt" & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample.
Data processing We carried out image and data analysis using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Justification of these procedures is presented in Tokuyasu et al. (in preparation). 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. Data were derived from two different versions of arrays: HumArray2.0 and HumArray3.1. For compatibility, data are presented in the HumArray 3.1 format.
 
Submission date Nov 08, 2006
Last update date Oct 08, 2007
Contact name Donna G Albertson
E-mail(s) albertson@ucsf.edu
Phone 415-502-8463
Organization name University of California San Francisco
Department Comprihensive Cancer Center
Street address Box 0808
City San Francisco
State/province CA
ZIP/Postal code 94143-0808
Country USA
 
Platform ID GPL4421
Series (1)
GSE6262 Genome Position and Gene Amplification

Data table header descriptions
ID_REF
VALUE LOG2RATIO, mean of log base 2 of LIN_RATIO
LIN_RATIO Mean of replicate Cy3/Cy5 ratios
LOG2STDDEV Standard deviation of VALUE
N_REPLIC Number of replicate spot measurements

Data table
ID_REF VALUE LIN_RATIO LOG2STDDEV N_REPLIC
1 0
2 0
3 -0.024057 0.983463 0.02381 3
4 -0.041658 0.971538 0.018329 3
5 -0.0051 0.996471 0.006244 3
6 0
7 0
8 0.060023 1.042482 0.042397 3
9 0.086337 1.061671 0.025112 3
10 -0.040372 0.972404 0.024701 3
11 0.002031 1.001409 0.022331 3
12 -0.051183 0.965144 0.096351 3
13 0.025699 1.017973 0.013291 3
14 0.098827 1.070902 0.020576 3
15 0.068756 1.048812 0.012997 2
16 0.118125 1.085323 0.032171 3
17 0.007905 1.005494 0.029241 3
18 0.126859 1.091914 0.044648 3
19 0.058168 1.041143 0.028556 3
20 0.112169 1.080852 0.020137 3

Total number of rows: 2464

Table truncated, full table size 71 Kbytes.




Supplementary file Size Download File type/resource
GSM143870_CY3.tif.gz 1.9 Mb (ftp)(http) TIFF
GSM143870_CY5.tif.gz 1.9 Mb (ftp)(http) TIFF
GSM143870_DAPI.tif.gz 2.0 Mb (ftp)(http) TIFF
GSM143870_spot.txt.gz 695.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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