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Sample GSM302898

Query DataSets for GSM302898

Status

Public on Oct 04, 2008

Title

BT3

Sample type

genomic

Source name

Breast carcinoma

Organism

Characteristics

Gender: Female

Extracted molecule

genomic DNA

Extraction protocol

Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and repeated phenol-chloroform extraction.

Label

C-Bio and A-DNP

Label protocol

Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

Hybridization protocol

RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

Scan protocol

After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

Description

Genomic DNA extracted from breast tumors was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

Data processing

Image data was analyzed using Beadstudio 3.1.3 with GT module 3.2.33 (Illumina).

Submission date

Jul 02, 2008

Last update date

Oct 04, 2008

Contact name

Johan Staaf

Organization name

SCIBLU - Swegene Centre for Integrative Biology at Lund University

Street address

Medicon Village

City

Lund

ZIP/Postal code

SE-223 81

Country

Sweden

Platform ID

Series (1)

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

Data table header descriptions
ID_REF
VALUE	Genotype: AA,AB,BB,or NC (no call)
GC_SCORE	Beadstudio confidence score
Theta	Beadstudio genotype metric
R	Beadstudio intensity metric
B_Allele_Freq	Beadstudio estimate of B allele frequency
Log_R_Ratio	Beadstudio metric for signal intensity

Data table
ID_REF	VALUE	GC_SCORE	Theta	R	B_Allele_Freq	Log_R_Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0	AA	0.3197343	0.006295365	6.168365	0.0005793257	0.4340365
MitoA10551G-13273286_T_F_IFB1141639111:0	AA	0.298474	0.02694375	7.892146	0.003654831	0.4950458
MitoA11252G-13273288_B_R_IFB1141661584:0	AA	0.329167	0.02629697	7.037316	0.008785129	0.286189
MitoA11468G-13273289_B_R_IFB1141719645:0	AA	0.3187215	0.02089008	8.917142	0.004183454	0.5097557
MitoA11813G-13273292_T_F_IFB1141667833:0	AA	0.2514375	0.0616666	6.278789	0.02043877	0.2722683
MitoA12309G-13273294_T_F_IFB1141664161:0	AA	0.2884996	0.02051028	6.112592	0	0.3043218
MitoA13106G-13273298_B_R_IFB1141641623:0	AA	0.3484128	0.01629472	1.970598	0	0.3299721
MitoA13264G-13273299_T_F_IFB1141660858:0	AA	0.2567114	0.03940718	8.11949	0.01276803	0.2703221
MitoA13781G-13273301_T_F_IFB1141687043:0	AA	0.3457177	0.03906345	1.791958	0	0.4920097
MitoA14234G-13273304_T_F_IFB1141674277:0	AA	0.3183387	0.01852514	4.626636	0.000786134	0.4833336
MitoA14583G-13273306_T_F_IFB1141688843:0	AA	0.329661	0.009473607	3.862606	0	0.7685766
MitoA15219G-13273311_T_F_IFB1141717824:0	AA	0.290874	0.09338295	6.190433	0.04337154	0.2621944
MitoA15245G-13273312_B_R_IFB1141677374:0	AA	0.319456	0.05800659	3.060153	0.02017083	0.1809487
MitoA15302G-13273313_T_F_IFB1141686491:0	BB	0.2735513	0.8019655	4.487495	0.9382495	0.23544
MitoA15759G-13273316_B_R_IFB1141715135:0	AA	0.3469829	0.02114267	6.16572	0.01068984	-0.04220777
MitoA15925G-13273318_T_F_IFB1141694300:0	AA	0.2904017	0.04128856	5.728662	0.0113548	0.5399933
MitoA16163G-13273319_T_F_IFB1141711520:0	NC	0.2471609	0.8376675	4.819956	0.9443282	0.1647119
MitoA16164G-13273320_T_F_IFB1141715312:0	NC	0.05917217	0.6475874	0.627664	0.6985759	-2.560582
MitoA1738G-13273322_T_F_IFB1141639534:0	AA	0.3015448	0.03109079	7.750114	0.01246986	0.3399161
MitoA3349G-13273328_T_F_IFB1141711832:0	AA	0.2904017	0.04322998	9.261428	0.01405482	0.3948469

Total number of rows: 561466

Table truncated, full table size 46827 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

Processed data provided as supplementary file

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