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GEO accession:
Sample GSM313931
Query DataSets for GSM313931
Status
Public on Oct 10, 2008
Title
NT124_250K_NSP
Sample type
genomic
Source Name
samples from primary neuroblastoma cases
Organism(s)
Homo sapiens
Characteristics
neuroblastoma
Extracted molecule
genomic DNA
Extraction protocol
standard DNA extraction
Label
biotin phytoerythrin
Label protocol
Affymetrix standard
Hybridization protocol
Affymetrix standard protocol
Scan protocol
Affymetrix standard protocol
Description
stage 4
Data processing
Copy number analyzer CNAG and allele specific copy number analysis algorithm AsCNAR 3.0
Submission date
Aug 19, 2008
Contact name
Yuyan Chen
E-mail(s)
chen-yuyan@umin.ac.jp
Organization name
University of Tokyo
Department
Pediatrics
Street address
Hongo7-3-1, Bunkyo-ku
City
Tokyo
ZIP/Postal code
113-8655
Country
Japan
Platform ID
GPL3718
Series (1)
GSE12494
SNP data from Neuroblastoma samples
Data table header descriptions
ID_REF
log2ratio_AB
raw signal ratios
log2ratio_A
raw signal ratios
log2ratio_B
raw signal ratios
N_AB
total copy number inferred from raw signal ratios (log 2 ratio AB) based on hidden Markov
N_A
allele specific copy number inferred from raw signal ratios (log 2 ratio A) based on hidden Markov
N_B
allele specific copy number inferred from raw signal ratios (log 2 ratio B) based on hidden Markov
VALUE
SNP call for the indicated SNP
Call_reference
Data table
ID_REF
log2ratio_AB
log2ratio_A
log2ratio_B
N_AB
N_A
N_B
VALUE
Call_reference
SNP_A-1886933
-0.174084
0.165115
-1.155976
2
1
1
BB
1
SNP_A-1902458
0.310039
0.830397
-0.511880
2
2
1
AB
2
SNP_A-2131660
0.050392
0.152168
-0.059113
2
2
1
AB
2
SNP_A-4221087
-0.008884
0.000000
0.000000
2
1
1
AA
1
SNP_A-1884606
-0.027164
0.000000
0.000000
2
0
0
AA
1
SNP_A-2235839
0.216964
0.438665
-0.045103
2
2
1
AB
2
SNP_A-2218153
0.091024
0.107695
0.074158
2
2
1
AB
2
SNP_A-1919019
-0.033260
0.354919
-0.723958
2
1
1
BB
1
SNP_A-1815933
-0.071854
0.000000
0.000000
2
1
1
BB
1
SNP_A-2115098
0.095138
0.638700
-0.951076
2
1
1
AA
1
SNP_A-2264565
0.124918
0.469525
-1.158264
2
1
1
BB
1
SNP_A-1788728
0.008320
0.000000
0.000000
2
1
1
BB
1
SNP_A-4218776
0.032249
0.000000
0.000000
2
0
0
AA
1
SNP_A-2082194
0.023201
0.275531
-0.282817
2
1
1
AB
2
SNP_A-2135694
-0.043162
0.459764
-1.462584
2
1
1
BB
1
SNP_A-4220764
-0.236442
-0.149758
-0.328669
2
1
1
AB
2
SNP_A-1796345
0.016411
0.000000
0.000000
2
1
1
BB
1
SNP_A-1789472
-0.155261
0.003475
-0.333647
2
1
1
AB
2
SNP_A-1934233
0.109865
0.000000
0.000000
2
1
1
BB
1
SNP_A-4207031
-0.387711
0.651042
-1.415466
2
1
1
AA
1
Total number of rows:
262264
Table truncated, full table size
13587 Kbytes
.
Supplementary file
Size
Download
File type/resource
GSM313931.CEL.gz
27.1 Mb
(ftp)
(http)
CEL
GSM313931.CHP.gz
433.3 Kb
(ftp)
(http)
CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file
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