GEO help: Mouse over screen elements for information.
Status
Public on Dec 01, 2012
Title
Whole blood 98
Sample type
genomic
Source name
Whole blood
Organism
Homo sapiens Characteristics
gender: M
Extracted molecule
genomic DNA
Extraction protocol
Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)
Label
Biotin-NTP
Label protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Hybridization protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Scan protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Description
sample id: 2740
Data processing
Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips
Submission date
Sep 30, 2012
Last update date
Dec 01, 2012
Contact name
Boyko Kabakchiev
Organization name
Mount Sinai Hospital
Department
Samuel Lunenfeld Research Institute
Lab
Silverberg Lab
Street address
60 Murray Street, Room L3-004
City
Toronto
State/province
Ontario
ZIP/Postal code
M5T 3L9
Country
Canada
Platform ID
GPL13135 Series (2)
GSE41238 eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Illumina SNP)
GSE41269 eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine
Data table header descriptions ID_REF VALUE SNP Calls
Top Geno HumanOmniExpress_12v1: Top Geno in NN format where N equals A, T, C, G, - ; HumanOmni2.5-Quad_4v1: Top Alleles in NN format where N equals A, T, C, G, -
Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio
Data table ID_REF VALUE Top Geno Theta R X Raw Y Raw X Y B Allele Freq Log R Ratio rs1000000
BB
GG
0.995
1.490
165
15435
0.011
1.478
1.0000
-0.0224
rs1000002
NC
NC
0.384
1.074
5657
4503
0.636
0.438
0.4525
0.0949
rs10000023
BB
CC
0.983
1.683
471
17108
0.045
1.638
1.0000
-0.0341
rs1000003
AB
AG
0.474
0.939
4365
4620
0.489
0.450
0.5214
-0.5469
rs10000030
NC
NC
0.765
0.533
1194
3677
0.149
0.385
0.4778
0.0770
rs10000037
BB
GG
0.974
0.959
356
8790
0.038
0.921
1.0000
0.0842
rs10000041
AA
AA
0.028
1.497
11222
651
1.433
0.064
0.0082
-0.2001
rs10000042
BB
GG
0.975
0.946
365
9512
0.036
0.911
1.0000
0.1382
rs10000049
AA
AA
0.020
1.265
12357
487
1.227
0.038
0.0000
0.1009
rs1000007
AB
AG
0.500
1.527
6018
7305
0.763
0.764
0.4871
0.1200
rs10000073
AA
AA
0.015
0.957
9422
299
0.935
0.023
0.0000
-0.2189
rs10000081
AA
AA
0.026
0.809
7054
354
0.777
0.032
0.0000
-0.2959
rs10000092
AA
AA
0.021
0.739
6494
263
0.715
0.023
0.0000
-0.0845
rs10000105
BB
GG
0.974
1.236
575
13340
0.048
1.189
1.0000
0.1605
rs10000119
BB
GG
0.986
1.218
296
12443
0.027
1.191
1.0000
-0.0246
rs10000124
BB
CC
0.983
1.228
341
12491
0.032
1.196
0.9987
-0.1840
rs10000154
AB
AG
0.491
1.047
4840
5399
0.531
0.516
0.4396
0.2570
rs1000016
AA
AA
0.027
0.690
5191
293
0.662
0.028
0.0000
-0.0701
rs10000160
BB
GG
0.940
0.772
640
7375
0.067
0.706
0.9660
-0.0487
rs10000169
AB
AG
0.509
1.511
6786
8017
0.745
0.766
0.4720
0.1695
730525 45909 Kbytes .Supplementary data files not provided Processed data included within Sample table
