GEO help: Mouse over screen elements for information.
Status
Public on Dec 01, 2012
Title
Whole blood 119
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 HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Hybridization protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Scan protocol
Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips
Description
sample id: 4844
Data processing
Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips
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
0.404
2.105
12835
11509
1.213
0.892
0.4788
-0.0495
rs1000002
NC
NC
0.436
0.936
5375
5327
0.516
0.421
0.5126
-0.0927
rs10000023
AB
AC
0.493
2.200
11779
14021
1.112
1.087
0.5349
-0.0569
rs1000003
AA
AA
0.020
1.002
10070
428
0.971
0.031
0.0000
-0.3751
rs10000030
NC
NC
0.985
0.642
180
7456
0.014
0.628
1.0000
0.0896
rs10000037
BB
GG
0.960
0.888
532
9929
0.052
0.836
0.9902
-0.0353
rs10000041
AA
AA
0.022
1.422
12783
598
1.375
0.047
0.0000
-0.2748
rs10000042
BB
GG
0.979
0.911
351
11351
0.030
0.881
1.0000
0.0853
rs10000049
AA
AA
0.017
1.397
16154
548
1.360
0.037
0.0000
0.2455
rs1000007
AB
AG
0.504
1.479
6863
8852
0.735
0.744
0.4910
0.0732
rs10000073
AA
AA
0.017
0.953
11028
377
0.928
0.025
0.0004
-0.2266
rs10000081
AA
AA
0.020
0.758
7772
316
0.734
0.023
0.0000
-0.3892
rs10000092
AB
AG
0.537
0.795
3983
5427
0.375
0.421
0.5341
-0.0615
rs10000105
BB
GG
0.980
1.280
530
17347
0.039
1.241
1.0000
0.2135
rs10000119
BB
GG
0.985
1.271
343
16005
0.028
1.243
1.0000
0.0364
rs10000124
BB
CC
0.985
1.219
330
15344
0.027
1.191
1.0000
-0.1928
rs10000154
AB
AG
0.566
0.852
4058
6074
0.382
0.471
0.5142
-0.0515
rs1000016
AB
AG
0.561
0.621
2645
4049
0.281
0.340
0.5205
-0.2464
rs10000160
BB
GG
0.964
0.735
448
8961
0.039
0.695
0.9956
-0.1113
rs10000169
AB
AG
0.514
1.555
8060
10253
0.760
0.795
0.4772
0.2088
730525 46057 Kbytes .Supplementary data files not provided Processed data included within Sample table
