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Sample GSM929765

Query DataSets for GSM929765

Status

Public on May 11, 2012

Title

Patient5_mother

Sample type

genomic

Source name

DNA from blood, patient 5 mother

Organism

Characteristics

individual: patient 5 mother
gender: female
tissue: blood
treatment: none
disease state: not applicable

Extracted molecule

genomic DNA

Extraction protocol

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

Label

Biotin (C, G), DNP (A,T)

Label protocol

200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation, the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol 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 an iScan (Illumina).

Description

Genomic DNA extracted from sample was genotyped using the Illumina HumanHap300v1 Genotyping BeadChip.

Data processing

Data processing was done using GenomeStudio (Illumina).

Submission date

May 10, 2012

Last update date

May 11, 2012

Contact name

Wigard Kloosterman

E-mail(s)

w.kloosterman@umcutrecht.nl

Organization name

University Medical Center Utrecht

Street address

Universiteitsweg 100

City

Utrecht

ZIP/Postal code

3584 CG

Country

Netherlands

Platform ID

Series (1)

Analysis of copy number changes and complex rearrangements in patients with congenital abnormalities

Data table header descriptions
ID_REF
VALUE	Genotype: AA, AB, BB, or NC (no 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
rs10000010-124_B_F_1137743663	BB	0.8891134	0.9932148	0.5670118	1	-0.2741854
rs10000023-124_B_F_1136477253	AB	0.819921	0.571855	2.205265	0.538108	-0.001028307
rs10000030-124_B_R_1137703207	BB	0.8305866	1	0.6314048	1	-0.061908
rs1000007-124_T_F_1135763903	AB	0.9373029	0.6112557	0.9760015	0.5487812	-0.2158174
rs10000092-124_T_R_1136459723	AB	0.82003	0.5352857	0.7564228	0.4984604	0.04471628
rs10000121-124_B_R_1136471760	AA	0.8743589	0.00	0.2711243	0.00	-0.09417994
rs1000014-124_B_R_1136184019	BB	0.8471238	0.9797254	1.029634	1	-0.09605556
rs10000141-124_T_F_1137734411	BB	0.9105554	0.9998141	0.7706395	1	-0.2224178
rs1000016-124_B_R_1135100999	AA	0.9132724	0.00	1.294009	0.00	-0.007704635
rs10000169-124_T_R_1135612081	AB	0.8942093	0.5934016	1.186867	0.4821585	0.03336754
rs1000022-124_B_F_1135126284	AB	0.9479493	0.6380801	0.8292556	0.5472063	-0.06202012
rs10000272-124_T_R_1136539894	AA	0.8459769	0.00	1.179744	0.00	-0.5039365
rs10000282-124_T_R_1136743500	BB	0.9291006	0.9906046	1.030529	1	-0.3146476
rs10000300-124_T_R_1136213300	AB	0.8549833	0.6270993	0.4634961	0.5801721	-0.1367201
rs1000031-124_B_F_1135583872	BB	0.853794	0.9526083	0.9946546	1	-0.2556839
rs1000032-124_B_R_1136145093	BB	0.8087894	0.9912297	0.9305147	1	-0.1275166
rs10000388-124_B_F_1135932472	BB	0.8960621	0.9965571	1.322439	1	0.1455928
rs1000040-124_T_F_1136126513	AA	0.9128333	0.01315737	0.5752557	0.00	-0.1639222
rs1000041-124_T_F_1136188169	BB	0.8436726	0.9872023	1.206202	1	-0.0138328
rs10000432-124_T_R_1135756304	BB	0.8417868	0.9987401	0.8637782	1	-0.02050939

Total number of rows: 317503

Table truncated, full table size 24199 Kbytes.

Supplementary data files not provided

Processed data included within Sample table

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