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Sample GSM622249 Query DataSets for GSM622249
Status Public on Nov 13, 2010
Title PCNSlymphoma_rep2
Sample type genomic
 
Channel 1
Source name PCNSL tumor sample
Organism Homo sapiens
Characteristics tissue: Brain
Extracted molecule genomic DNA
Extraction protocol Fresh-frozen samples were obtained from 12 patients with primary central nervous system diffuse large B cell lymphoma and 13 peripheral blood from healthy men.
Label Cy5
Label protocol 1.5 ug of test DNA and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI) and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown,MD). Test sample DNA and reference DNA were labeled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
 
Channel 2
Source name Reference DNA
Organism Homo sapiens
Characteristics tissue: Human reference DNA
Extracted molecule genomic DNA
Extraction protocol Fresh-frozen samples were obtained from 12 patients with primary central nervous system diffuse large B cell lymphoma and 13 peripheral blood from healthy men.
Label Cy3
Label protocol 1.5 ug of test DNA and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI) and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown,MD). Test sample DNA and reference DNA were labeled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.
 
 
Hybridization protocol After probe denaturation and preannealing with Cot-1 DNA, hybridization was performed at 65oC with rotation for 40 hours.
Scan protocol Scanned on an Agilent DNA microarray scanner.
Description CGH
Data processing Data were obtained using Agilent Feature Extraction Software 9 and analyzed with Agilent CGH Analytics 4.0 Software.
 
Submission date Nov 12, 2010
Last update date Nov 12, 2010
Contact name Chang Ohk Sung
Organization name Asan Medical Center
Department Pathology
Street address Song-Pa gu,Pung-nap dong
City Seoul
ZIP/Postal code 05505
Country South Korea
 
Platform ID GPL8841
Series (2)
GSE25298 Genomic aberrations in primary central nervous system lymphoma (PCNSL)
GSE25299 Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy5/Cy3) representing test/reference (Aberration Algorithm: ADM-1).

Data table
ID_REF VALUE
A_14_P112718 -1.047877192
A_14_P201353 -0.603381634
A_14_P108353 1.465313911
A_14_P129881 0.346393615
A_14_P114030 -0.332330585
A_14_P139527 0.03173589
A_14_P118340 0.477773368
A_14_P106890 0.04447075
A_14_P122641 -0.275736719
A_14_P107170 0.515276015
A_14_P100766 0.862541914
A_14_P118104 1.41780293
A_14_P117253 0.327368796
A_14_P129407 0.375625759
A_14_P200001 0.34976542
A_14_P103811 0.670342207
A_14_P119666 0.796611309
A_14_P100799 1.812632799
A_14_P121179 1.129820585
A_14_P115318 -0.072753079

Total number of rows: 42116

Table truncated, full table size 1042 Kbytes.




Supplementary file Size Download File type/resource
GSM622249.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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