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Status
Public on Dec 01, 2012
Title
Whole blood 162
Sample type
genomic
Source name
Whole blood
Organism
Homo sapiens Characteristics
gender: F
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: 142
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
AB
AG
0.424
2.173
11199
11119
1.216
0.957
0.5029
-0.0078
rs1000002
NC
NC
0.046
0.882
7379
735
0.823
0.059
0.0229
-0.2188
rs10000023
AB
AC
0.479
2.136
10169
11984
1.104
1.032
0.5212
-0.1099
rs1000003
AA
AA
0.022
0.981
8493
449
0.948
0.033
0.0000
-0.4069
rs10000030
NC
NC
0.965
0.589
288
5978
0.030
0.559
0.9809
-0.0132
rs10000037
AB
AG
0.494
0.920
3766
4897
0.465
0.455
0.5263
-0.2522
rs10000041
AA
AA
0.024
1.336
10351
585
1.288
0.048
0.0018
-0.3645
rs10000042
BB
GG
0.945
0.615
490
6563
0.049
0.566
0.9720
-0.5011
rs10000049
AA
AA
0.016
1.293
13076
514
1.261
0.032
0.0000
0.1341
rs1000007
AA
AA
0.009
1.221
9673
251
1.204
0.017
0.0000
-0.0494
rs10000073
AA
AA
0.015
0.953
9657
362
0.930
0.023
0.0000
-0.2261
rs10000081
AA
AA
0.016
0.810
7275
269
0.789
0.020
0.0000
-0.2921
rs10000092
AB
AG
0.526
0.771
3433
4666
0.370
0.401
0.5221
-0.1094
rs10000105
BB
GG
0.987
1.121
307
13860
0.022
1.099
1.0000
0.0263
rs10000119
BB
GG
0.982
1.331
377
15003
0.036
1.295
1.0000
0.1016
rs10000124
BB
CC
0.982
1.263
360
14233
0.034
1.229
0.9981
-0.1441
rs10000154
AB
AG
0.566
0.958
3975
6145
0.429
0.529
0.5140
0.1167
rs1000016
AA
AA
0.030
0.653
5021
357
0.623
0.030
0.0029
-0.1501
rs10000160
BB
GG
0.971
0.636
292
7052
0.027
0.608
1.0000
-0.3169
rs10000169
AA
AA
0.021
1.360
12099
563
1.315
0.044
0.0000
0.2557
730525 46001 Kbytes .Supplementary data files not provided Processed data included within Sample table
