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Status
Public on Dec 01, 2012
Title
Whole blood 44
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 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: 4710
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
0.988
1.507
364
18089
0.028
1.478
0.9975
-0.0140
rs1000002
NC
NC
0.412
0.764
4404
4010
0.436
0.329
0.4873
-0.3926
rs10000023
AA
AA
0.019
1.979
19570
862
1.920
0.058
0.0000
-0.0296
rs1000003
AB
AG
0.470
1.247
6604
7221
0.653
0.594
0.5181
-0.1402
rs10000030
NC
NC
0.967
0.616
333
6600
0.030
0.586
0.9851
0.0500
rs10000037
BB
GG
0.972
0.920
422
9924
0.039
0.881
1.0000
0.0229
rs10000041
AA
AA
0.026
1.680
14319
870
1.614
0.066
0.0048
-0.0337
rs10000042
BB
GG
0.974
0.860
401
10106
0.034
0.826
1.0000
0.0002
rs10000049
AA
AA
0.025
1.292
14085
773
1.243
0.049
0.0023
0.1293
rs1000007
AB
AG
0.508
1.412
6230
8103
0.697
0.715
0.4952
0.0044
rs10000073
AA
AA
0.013
0.984
10928
364
0.965
0.020
0.0000
-0.1780
rs10000081
AB
AG
0.551
0.945
4467
6268
0.434
0.510
0.5301
-0.1844
rs10000092
AA
AA
0.020
0.800
7931
344
0.776
0.024
0.0000
0.0317
rs10000105
BB
GG
0.977
1.225
611
15535
0.043
1.182
1.0000
0.1484
rs10000119
BB
GG
0.984
1.317
390
15728
0.031
1.286
1.0000
0.0871
rs10000124
BB
CC
0.985
1.242
361
14842
0.029
1.213
1.0000
-0.1658
rs10000154
AB
AG
0.538
0.952
4604
6197
0.448
0.504
0.4842
0.1090
rs1000016
BB
GG
0.966
0.712
387
7616
0.036
0.676
0.9924
0.0557
rs10000160
BB
GG
0.982
0.752
261
8943
0.020
0.732
1.0000
-0.0703
rs10000169
BB
GG
0.993
1.237
214
14956
0.014
1.223
1.0000
0.0958
730525 46062 Kbytes .Supplementary data files not provided Processed data included within Sample table
