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Sample GSM1603776 Query DataSets for GSM1603776
Status Public on Jun 01, 2016
Title Relapsing_DLBCL_relapse (case5)
Sample type genomic
 
Channel 1
Source name FFPE tissue biopsy
Organism Homo sapiens
Characteristics disease state: Diffuse large B cell lymphoma (DLBCL)
specimen: Relapsing DLBCL relapse
case: 5
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_case5_relapse
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 1.0221292
A_18_P10001325 0.8993155
A_18_P10001390 1.2530649
A_18_P10001457 0.9149276
A_18_P10001545 -0.8030095
A_16_P15001543 1.2087202
A_16_P15001594 -0.45756125
A_16_P00000099 1.5164633
A_16_P00000136 -0.04961873
A_16_P15001756 -0.015569456
A_16_P00000179 1.1624639
A_16_P00000195 0.48685813
A_16_P15001886 -0.42173958
A_16_P00000237 -0.4529512
A_16_P15001967 1.6789304
A_16_P00000285 -0.3436551
A_16_P00000311 -0.2503395
A_16_P15002151 0.7632425
A_18_P17422640 1.5243697
A_16_P00000357 2.0101445

Total number of rows: 169293

Table truncated, full table size 4187 Kbytes.




Supplementary file Size Download File type/resource
GSM1603776_rel_rel_case5.txt.gz 18.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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