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Status
Public on Dec 01, 2012
Title
Whole blood 27
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 HumanOmni Express and HumanOmni2.5-Quad Beadchips
Hybridization protocol
Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips
Scan protocol
Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips
Description
sample id: 4676
Data processing
GenomeStudio was used for processing the samples - version 1.8.4 for OmniExpress chips and version 1.9.4 for Omni2.5 chips.
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
0.992
1.434
303
21278
0.019
1.415
1.0000
-0.0815
rs1000002
NC
NC
0.981
1.133
494
16220
0.032
1.101
1.0000
0.4539
rs10000023
BB
CC
0.977
1.742
809
25274
0.061
1.681
1.0000
0.0099
rs1000003
AA
AA
0.029
1.142
12535
843
1.092
0.050
0.0000
-0.1895
rs10000030
NC
NC
0.961
0.565
381
7313
0.033
0.532
0.9677
-0.0666
rs10000037
BB
GG
0.972
0.834
429
10966
0.035
0.798
1.0000
-0.1195
rs10000041
AA
AA
0.032
1.452
14261
1063
1.381
0.070
0.0139
-0.2436
rs10000042
AB
AG
0.591
0.960
4870
8288
0.411
0.550
0.5136
-0.0542
rs10000049
AA
AA
0.020
1.352
17269
841
1.311
0.042
0.0000
0.1973
rs1000007
AA
AA
0.009
1.229
12504
317
1.212
0.017
0.0000
-0.0402
rs10000073
AA
AA
0.015
1.070
13778
523
1.045
0.025
0.0000
-0.0584
rs10000081
AB
AG
0.560
0.987
5292
8144
0.447
0.540
0.5401
-0.1168
rs10000092
AA
AA
0.024
0.790
8959
468
0.761
0.028
0.0000
0.0110
rs10000105
BB
GG
0.982
1.139
521
18150
0.031
1.108
1.0000
0.0464
rs10000119
BB
GG
0.983
1.296
475
18984
0.034
1.262
1.0000
0.0633
rs10000124
BB
CC
0.985
1.350
443
19838
0.031
1.319
1.0000
-0.0452
rs10000154
AB
AG
0.554
0.917
4975
7501
0.420
0.497
0.4993
0.0510
rs1000016
AA
AA
0.020
0.564
5646
266
0.547
0.017
0.0000
-0.3606
rs10000160
BB
GG
0.969
0.709
446
10170
0.033
0.676
1.0000
-0.1605
rs10000169
AB
AG
0.592
1.468
7424
12658
0.627
0.840
0.5602
0.1396
730525 46194 Kbytes .Supplementary data files not provided Processed data included within Sample table
