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Sample GSM1603799 Query DataSets for GSM1603799
Status Public on Jun 01, 2016
Title Non-relapsing_DLBCL_primary (case28)
Sample type genomic
 
Channel 1
Source name Frozen tissue biopsy
Organism Homo sapiens
Characteristics disease state: Diffuse large B cell lymphoma (DLBCL)
specimen: Non-relapsing DLBCL primary
case: 28
Treatment protocol na
Growth protocol na
Extracted molecule genomic DNA
Extraction protocol H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.
Label cy5
Label protocol A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
 
Channel 2
Source name Reference pooled 46XX
Organism Homo sapiens
Characteristics tissue: pooled normal (46,XX) reference (Promega)
Treatment protocol na
Growth protocol na
Extracted molecule genomic DNA
Extraction protocol H&E- and CD20-stained sections of FFPE blocks or fresh-frozen tissue were reviewed to evaluate tumor content. Only tissues with >70% tumor content were used. Depending on the distribution of tumor cells, 25µm-thick sections were cut or punches were taken from the tumor-rich tissue areas. Prior to overnight Proteinase K digestion, paraffin sections were deparaffinized and rehydrated by serial xylene and ethanol washes, respectively. Genomic DNA (gDNA) was extracted by automation using Maxwell® 16 FFPE plus LEV DNA Purification Kit. gDNA from samples with extremely scarce tumor material was isolated by the phenol-chloroform extraction as described previously22. Yields were quantified by the Qubit assay.
Label cy3
Label protocol A 100-500 nanogram aliquot of each sample and reference DNA was heat digested then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.
 
 
Hybridization protocol Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 25 rpm for at least 24 hours then washed according to array supplier's (Agilent)protocol
Scan protocol All arrays were scanned using an Agilent 2565C Scanner and default settings for CGH.
Description BIP_case28_primary
Data processing Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then visulaized and analyzed using Agilent Genomic Workbench v7.0 and the ADM2 algorithm.
 
Submission date Feb 06, 2015
Last update date Jun 01, 2016
Contact name Darius Juskevicius
E-mail(s) JuskeviciusD@uhbs.ch
Organization name Institute of Pathology
Department Molecuar Pathology
Street address Schoenbeinstr. 40
City Basel
ZIP/Postal code 4031
Country Switzerland
 
Platform ID GPL10150
Series (1)
GSE65720 Clonal relationship of relapsing diffuse large B-cell lymphoma

Data table header descriptions
ID_REF
VALUE normalized log2 ratios (sample/reference)

Data table
ID_REF VALUE
A_16_P15000916 0.76509583
A_18_P10001325 0.39194697
A_18_P10001390 0.046657965
A_18_P10001457 0.10285659
A_18_P10001545 0.24899891
A_16_P15001543 0.9053077
A_16_P15001594 0.084041715
A_16_P00000099 -0.036612153
A_16_P00000136 -0.17715338
A_16_P15001756 -0.13913453
A_16_P00000179 -0.30152965
A_16_P00000195 -0.4419765
A_16_P15001886 -0.008354694
A_16_P00000237 -0.41883534
A_16_P15001967 -0.34668577
A_16_P00000285 0.015716702
A_16_P00000311 0.35535377
A_16_P15002151 0.125733
A_18_P17422640 0.13967589
A_16_P00000357 0.27267945

Total number of rows: 169293

Table truncated, full table size 4277 Kbytes.




Supplementary file Size Download File type/resource
GSM1603799_pri_non-rel_case8.txt.gz 18.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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