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Sample GSM269798 Query DataSets for GSM269798
Status Public on Feb 29, 2008
Title Agilent 244k Chip 1
Sample type genomic
 
Channel 1
Source name JW DNA extracted from blood
Organism Homo sapiens
Characteristics Blood from JW
Biomaterial provider 2 samples from JW
Extracted molecule genomic DNA
Extraction protocol DNA extracted from blood using FlexiGene DNA kit from Qiagen
Label Cy5
Label protocol The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of Cy5-dCTP following standard Agilent protocal
 
Channel 2
Source name Reference DNA extracted from standard reference Caucasian male blood
Organism Homo sapiens
Characteristics Blood from standard reference Caucasian male
Biomaterial provider Kleberg Cytogenetics Laboratory, Baylor College of Medicine
Extracted molecule genomic DNA
Extraction protocol DNA extracted from blood using FlexiGene DNA kit from Qiagen
Label Cy3
Label protocol The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of Cy3-dCTP (PerkinElmer) following standard Agilent protocal
 
 
Hybridization protocol Experimental and reference targets for each hybridization were purified, pooled and incubated with human Cot-1 DNA (Invitrogen) and Blocking Agent (Agilent Technologies, Inc.)
Scan protocol Slides were scanned into image files using an Axon microarray scanner (GenePix 4000B from Axon Instruments, Union City, CA, USA)
Description CNV data for JW (Agilent Human Genome CGH 244K Array)
Data processing Data was analyzed using the CGH Analytics software (Agilent Technologies, Inc.)
 
Submission date Feb 28, 2008
Last update date Feb 28, 2008
Contact name Omar Alvi
E-mail(s) [email protected]
Organization name Baylor College of Medicine
Department Human Genome Sequencing Center
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL4544
Series (1)
GSE10668 The Complete Genome of a Single Individual by Massively Parallel DNA Sequencing

Data table header descriptions
ID_REF
VALUE log(REDsignal/GREENsignal) per feature (processed signals used).
LogRatioError error of the log ratio calculated according to the error model chosen.
PValueLogRatio Significance level of the Log Ratio computed for a feature.
gProcessedSignal Dye-normalized signal after surrogate algorithm, green channel, used for computation of log ratio.
rProcessedSignal Dye-normalized signal after surrogate algorithm, red channel, used for computation of log ratio.

Data table
ID_REF VALUE LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal
1 2.304955993e-002 6.149361941e-002 7.077880315e-001 2.930988e+003 3.090748e+003
2 -2.505264089e-001 3.169831222e-001 4.293256076e-001 2.803247e+001 1.574472e+001
3 9.001841757e-002 5.049635867e-001 8.585131790e-001 1.144968e+001 1.408679e+001
4 -7.663729097e-002 6.246484099e-002 2.198651300e-001 8.043062e+002 6.741928e+002
5 -7.701910700e-003 6.166383391e-002 9.006014622e-001 1.227326e+003 1.205753e+003
6 -1.000765067e-001 6.615824306e-002 1.303599923e-001 3.254942e+002 2.585037e+002
7 -9.610199782e-002 6.245709383e-002 1.238804339e-001 1.030403e+003 8.258574e+002
8 4.850871971e-002 6.177132911e-002 4.322805907e-001 1.286956e+003 1.439039e+003
9 -8.103411612e-002 6.233842083e-002 1.936330364e-001 9.490064e+002 7.874719e+002
10 1.077826621e-001 8.587824235e-002 2.094556506e-001 8.048615e+001 1.031582e+002
11 -3.917806140e-003 6.180279382e-002 9.494543133e-001 9.744626e+002 9.657114e+002
12 -3.403739520e-002 6.171985469e-002 5.813032349e-001 1.323776e+003 1.223988e+003
13 5.487357805e-002 6.168295885e-002 3.736770697e-001 2.293325e+003 2.602191e+003
14 -6.142816152e-002 6.273651231e-002 3.275081993e-001 6.230075e+002 5.408354e+002
15 -7.023928472e-003 6.154977683e-002 9.091443689e-001 1.698681e+003 1.671429e+003
16 2.973498490e-002 6.393527257e-002 6.418745228e-001 3.680144e+002 3.940940e+002
17 2.029503013e-002 6.185471727e-002 7.428299746e-001 9.209316e+002 9.649891e+002
18 -3.308355830e-001 6.972970669e-002 2.089777149e-006 7.274928e+002 3.396199e+002
19 1.877259806e-003 6.177780975e-002 9.757581866e-001 1.004289e+003 1.008640e+003
20 -8.261122186e-002 6.236277907e-002 1.852746816e-001 9.493178e+002 7.848748e+002

Total number of rows: 243430

Table truncated, full table size 20458 Kbytes.




Supplementary file Size Download File type/resource
GSM269798.txt.gz 69.4 Mb (ftp)(http) TXT
Processed data included within Sample table
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