GEO help: Mouse over screen elements for information.
Status
Public on Feb 01, 2016
Title
blood-PTC_E11770
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: PTC
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
AB
0.002924
AB
3418.529541
3657.396973
SNP_A-1967418
BB
0.003153
BB
379.523407
812.457581
SNP_A-1969580
BB
0.007798
BB
699.487244
2774.217529
SNP_A-4263484
BB
0.001413
BB
670.317627
2062.575684
SNP_A-1978185
AA
0.015877
AA
2397.162354
431.053894
SNP_A-4264431
AB
0.005178
AB
1507.703857
1242.207153
SNP_A-1980898
NC
0.311081
AB
1115.146240
614.170715
SNP_A-1983139
AA
0.004535
AA
2468.549805
743.164917
SNP_A-4265735
AA
0.006101
AA
2921.650879
571.504883
SNP_A-1995832
AB
0.032035
AB
1454.586914
716.962952
SNP_A-1995893
AB
0.006382
AB
1543.102905
2209.524414
SNP_A-1997689
BB
0.005996
BB
935.794983
4642.533691
SNP_A-1997709
AA
0.004148
AA
1729.386475
287.401917
SNP_A-1997896
AA
0.005044
AA
1532.123413
506.852509
SNP_A-1997922
AB
0.017159
AB
940.002197
777.930481
SNP_A-2000230
AA
0.003033
AA
2308.366211
1212.980713
SNP_A-2000332
AA
0.009287
AA
3601.621582
1453.997925
SNP_A-2000337
AA
0.003735
AA
1226.891846
447.026123
SNP_A-2000342
AA
0.010553
AA
4583.138672
1086.111206
SNP_A-4268173
AA
0.005088
AA
1479.202759
222.987503
909622 46148 Kbytes .Supplementary file Size Download File type/resource GSM1637335_E11770_GenomeWideSNP_6_.CEL.gz
25.0 Mb
(ftp) (http) CEL
GSM1637335_E11770_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.6 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
