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Status
Public on Dec 01, 2012
Title
Whole blood 2
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: 4719
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
AB
AG
0.416
2.030
10407
8452
1.149
0.881
0.4943
-0.1066
rs1000002
NC
NC
0.975
1.012
412
9101
0.038
0.974
0.9956
0.2870
rs10000023
AA
AA
0.015
1.913
16896
482
1.870
0.044
0.0000
-0.0758
rs1000003
BB
GG
0.986
0.891
235
8149
0.019
0.872
1.0000
-0.2434
rs10000030
NC
NC
0.769
0.614
1382
3949
0.169
0.445
0.4814
0.2765
rs10000037
BB
GG
0.968
0.900
396
7605
0.043
0.857
0.9977
-0.0113
rs10000041
AA
AA
0.028
1.425
10882
623
1.365
0.060
0.0075
-0.2713
rs10000042
AB
AG
0.568
1.080
4391
5728
0.482
0.598
0.4866
0.1209
rs10000049
AA
AA
0.025
1.223
11909
572
1.176
0.046
0.0025
0.0495
rs1000007
AB
AG
0.508
1.371
5429
6209
0.677
0.694
0.4950
-0.0376
rs10000073
AA
AA
0.020
1.050
10311
410
1.018
0.032
0.0029
-0.0876
rs10000081
AB
AG
0.543
0.918
3896
4698
0.428
0.490
0.5214
-0.2306
rs10000092
AA
AA
0.012
0.742
6594
169
0.728
0.014
0.0000
-0.0766
rs10000105
BB
GG
0.974
1.192
536
11755
0.047
1.145
1.0000
0.1072
rs10000119
BB
GG
0.984
1.281
333
11934
0.032
1.249
1.0000
0.0468
rs10000124
BB
CC
0.979
1.282
414
11861
0.041
1.242
0.9953
-0.1253
rs10000154
AA
AA
0.015
0.822
7279
213
0.804
0.019
0.0000
0.0319
rs1000016
BB
GG
0.983
0.702
194
6059
0.018
0.684
1.0000
0.0395
rs10000160
BB
GG
0.945
0.608
475
5350
0.048
0.559
0.9721
-0.3928
rs10000169
BB
GG
0.991
1.255
215
11815
0.018
1.237
1.0000
0.1161
730525 45873 Kbytes .Supplementary data files not provided Processed data included within Sample table
