GEO help: Mouse over screen elements for information.
Status
Public on Feb 01, 2016
Title
blood-MTC_5419
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens
Characteristics
phenotype: MTC tissue: peripheral blood
Treatment protocol
None
Growth protocol
None
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label
Biotin
Label protocol
As per manufacturer (Affymetrix)
Hybridization protocol
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and images were obtained using an Affymetrix GeneChip® Scanner 3000.
Data processing
CEL files were processed using Affymetrix Power Tools (APT v1.15.0) using Birdseed v2 calling algorithm.
Submission date
Mar 18, 2015
Last update date
Feb 01, 2016
Contact name
Joaquin Dopazo
E-mail(s)
jdopazo@cipf.es
Organization name
Centro de Investigacion Principe Felipe
Department
Systems Biology
Street address
Eduardo Primo Yúfera, 3
City
Valencia
State/province
Valencia
ZIP/Postal code
46012
Country
Spain
Platform ID
GPL6801
Series (1)
GSE67047
Genome-wide association and epistatic studies in sporadic medullary and juvenile papillary thyroid carcinomas
Data table header descriptions
ID_REF
PROBE SET NAME
VALUE
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE
FORCED CALL
SIGNAL A
Summarized signal
SIGNAL B
Summarized signal
Data table
ID_REF
VALUE
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B
SNP_A-2131660
BB
0.000759
BB
920.641541
4586.694336
SNP_A-1967418
BB
0.000843
BB
323.998749
741.745300
SNP_A-1969580
BB
0.003403
BB
1283.656494
4478.968262
SNP_A-4263484
BB
0.002984
BB
510.679443
1557.829834
SNP_A-1978185
AA
0.006648
AA
1865.872559
352.764191
SNP_A-4264431
AA
0.004505
AA
2131.707031
398.268311
SNP_A-1980898
BB
0.001628
BB
338.477264
866.101685
SNP_A-1983139
AA
0.004851
AA
3015.748535
628.218262
SNP_A-4265735
AB
0.002656
AB
1144.446899
1251.478516
SNP_A-1995832
BB
0.000927
BB
722.158325
2050.758545
SNP_A-1995893
BB
0.000575
BB
546.984802
2429.882568
SNP_A-1997689
BB
0.000773
BB
762.631714
3464.884766
SNP_A-1997709
AA
0.001742
AA
1507.390747
359.592072
SNP_A-1997896
BB
0.004071
BB
608.533936
1959.346313
SNP_A-1997922
AA
0.008914
AA
746.248901
373.304352
SNP_A-2000230
AA
0.002098
AA
2139.108643
1120.399292
SNP_A-2000332
AA
0.017720
AA
3817.930176
555.039551
SNP_A-2000337
AA
0.004388
AA
1574.301147
320.346252
SNP_A-2000342
AA
0.002629
AA
3582.869629
1050.052002
SNP_A-4268173
AA
0.000326
AA
1563.726685
350.909271
Total number of rows: 909622 Table truncated, full table size 46144 Kbytes .Supplementary file
Size
Download
File type/resource
GSM1636621_5419_GenomeWideSNP_6_.CEL.gz
28.1 Mb
(ftp) (http)
CEL
GSM1636621_5419_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http)
CHP
Processed data included within Sample table
Processed data provided as supplementary file