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Status
Public on Dec 01, 2012
Title
Whole blood 12
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: 4264
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
0.410
1.989
8723
7013
1.136
0.853
0.4865
-0.1335
rs1000002
NC
NC
0.379
1.097
4945
3559
0.654
0.443
0.4454
0.1258
rs10000023
AB
AC
0.479
2.301
9127
9140
1.188
1.113
0.5216
-0.0020
rs1000003
AA
AA
0.029
0.959
6904
357
0.917
0.042
0.0000
-0.4414
rs10000030
NC
NC
1.000
0.542
28
4169
0.000
0.542
1.0000
-0.1700
rs10000037
BB
GG
0.973
0.901
285
6637
0.037
0.864
1.0000
-0.0077
rs10000041
AB
AC
0.371
1.377
5692
4215
0.830
0.547
0.4829
-0.2757
rs10000042
BB
GG
0.958
0.945
470
7277
0.058
0.887
0.9896
0.1259
rs10000049
AA
AA
0.020
1.192
9896
349
1.156
0.037
0.0000
0.0154
rs1000007
AA
AA
0.009
1.290
8703
155
1.272
0.017
0.0000
0.0297
rs10000073
AA
AA
0.016
1.025
8562
252
0.999
0.026
0.0000
-0.1206
rs10000081
AA
AA
0.029
0.719
5281
267
0.688
0.031
0.0000
-0.4676
rs10000092
AB
AG
0.455
0.821
3387
3138
0.440
0.381
0.4472
-0.0171
rs10000105
BB
GG
0.981
1.231
345
10512
0.035
1.195
1.0000
0.1573
rs10000119
BB
GG
0.986
1.371
265
10994
0.030
1.340
1.0000
0.1452
rs10000124
BB
CC
0.988
1.159
199
9331
0.022
1.137
1.0000
-0.2624
rs10000154
AB
AG
0.597
0.932
3041
4417
0.394
0.538
0.5505
0.0850
rs1000016
AA
AA
0.007
0.545
3697
59
0.539
0.006
0.0000
-0.4093
rs10000160
BB
GG
0.983
0.642
154
5133
0.017
0.625
1.0000
-0.2975
rs10000169
AA
AA
0.018
1.339
9997
313
1.304
0.036
0.0000
0.2362
730525 45735 Kbytes .Supplementary data files not provided Processed data included within Sample table
