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Status
Public on Dec 01, 2012
Title
Whole blood 11
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: 3816
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
0.995
1.424
182
21159
0.011
1.412
1.0000
-0.0879
rs1000002
NC
NC
0.400
1.022
6466
6354
0.591
0.430
0.4729
0.0247
rs10000023
AB
AC
0.497
2.098
11691
15660
1.053
1.045
0.5392
-0.1220
rs1000003
AB
AG
0.468
1.125
6470
7876
0.591
0.534
0.5156
-0.2907
rs10000030
NC
NC
0.796
0.540
1349
5650
0.135
0.406
0.5170
0.0688
rs10000037
BB
GG
0.984
0.892
261
12096
0.022
0.871
1.0000
-0.0136
rs10000041
BB
CC
0.983
1.028
313
13916
0.026
1.002
1.0000
-0.1552
rs10000042
BB
GG
0.968
0.885
505
12635
0.042
0.843
1.0000
0.0373
rs10000049
AA
AA
0.026
1.205
14203
816
1.158
0.047
0.0032
0.0284
rs1000007
AA
AA
0.014
1.245
11941
405
1.219
0.026
0.0000
-0.0231
rs10000073
AA
AA
0.019
1.048
12475
557
1.017
0.031
0.0025
-0.0896
rs10000081
AA
AA
0.027
0.819
8703
525
0.786
0.033
0.0000
-0.2783
rs10000092
AB
AG
0.508
0.838
4603
6372
0.414
0.424
0.5026
0.0035
rs10000105
BB
GG
0.980
1.161
503
18162
0.035
1.126
1.0000
0.0731
rs10000119
BB
GG
0.984
1.346
421
19670
0.033
1.313
1.0000
0.1183
rs10000124
BB
CC
0.983
1.202
404
17533
0.032
1.170
0.9983
-0.2152
rs10000154
AB
AG
0.554
0.873
4441
7119
0.399
0.474
0.5002
-0.0203
rs1000016
AA
AA
0.018
0.614
5855
268
0.597
0.017
0.0000
-0.2390
rs10000160
BB
GG
0.977
0.725
311
10496
0.025
0.700
1.0000
-0.1256
rs10000169
AA
AA
0.015
1.221
13207
447
1.193
0.028
0.0000
0.1043
730525 46155 Kbytes .Supplementary data files not provided Processed data included within Sample table
