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Sample GSM566666 Query DataSets for GSM566666
Status Public on Jul 16, 2010
Title BRCAx Breast tumor 60312 4302743297_B DNA
Sample type genomic
 
Source name kConFab
Organism Homo sapiens
Characteristics tissue: Breast Tumour
mutation status: BRCAx
Extracted molecule genomic DNA
Extraction protocol Frozen sections of 10 um were macrodissected with a needle to ensure that the neoplastic content was >75%. DNA was extracted by the salting-out method followed by a phenol chloroform extraction
Label C-Bio and A-DNP
Label protocol Standard Illumina Infinium protocol
 
Hybridization protocol Standard Illumina hybridization protocol to CNV370 duo beadarrays
Scan protocol Standard Illumina scanning protocol
Description n/a
Data processing The samples were preprocessed in Illumina's Genomestudio
 
Submission date Jul 15, 2010
Last update date Jul 15, 2010
Contact name Nic Waddell
Organization name Queensland Centre for Medical Genomics
Street address St Lucia
City Brisbane
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL6986
Series (1)
GSE19177 Subtypes of familial breast tumors revealed by expression and copy number profiling

Data table header descriptions
ID_REF
VALUE genotype call
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
rs10000010-126_B_F_IFB1153208421:0 AA 0.9368909 0.004986201 0.7101226 0.004092088 -0.4104817
rs10000023-126_B_F_IFB1153358872:0 AA 0.8234195 0.05041688 2.262368 0.02053372 -0.1071195
rs10000030-120_B_R_IFB1137703207:0 BB 0.8158658 0.9948955 0.8055413 1 0.05268827
rs1000007-123_T_F_IFB1152225452:0 AA 0.8747823 0.02512709 0.9377857 0.01368347 0.09671998
rs10000092-123_T_R_IFB1153358875:0 AB 0.923982 0.608735 0.7994019 0.6141788 0.1467548
rs10000121-126_B_R_IFB1136471760:0 AA 0.852161 0.05925035 0.4980943 0.03962003 0.059221
rs1000014-126_B_R_IFB1136184019:0 AB 0.7254323 0.5193818 2.190778 0.5566108 0.08498643
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9976421 0.9418475 1 0.03157602
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.02977128 1.498142 0.02936156 -0.2469478
rs10000169-119_T_R_IFB1135612081:0 AA 0.8703538 0.02423242 1.096181 0.0136598 0.1211049
rs1000022-126_B_F_IFB1135126284:0 AB 0.8797732 0.6219823 1.139329 0.4902197 0.3833182
rs10000272-126_T_R_IFB1136539894:0 AA 0.8433531 0.04220021 1.626959 0.04306984 -0.2177336
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.9777937 0.9893489 0.9906356 -0.2839838
rs10000300-126_T_R_IFB1152704058:0 AB 0.858349 0.6560162 0.5659061 0.5821651 -0.300681
rs1000031-123_B_F_IFB1135583872:0 AB 0.8717313 0.4373429 2.197441 0.470956 -0.07517364
rs1000032-126_B_R_IFB1136145093:0 AB 0.3132744 0.6690961 1.307004 0.4571105 0.2226399
rs10000388-126_B_F_IFB1135932472:0 BB 0.9530174 0.9947191 1.109496 1 -0.02897163
rs1000040-126_T_F_IFB1152704061:0 AB 0.8484263 0.5379724 1.03647 0.439235 0.07643186
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9773283 1.341632 0.9954765 -0.06748588
rs10000432-126_T_R_IFB1135756304:0 BB 0.8544981 0.9384394 0.8779035 0.9337646 0.1579957

Total number of rows: 370404

Table truncated, full table size 31023 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record
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