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Sample GSM2144372 Query DataSets for GSM2144372
Status Public on Jun 01, 2016
Title Non-relapsing_DLBCL_primary (case36)
Sample type genomic
 
Channel 1
Source name FFPE tissue biopsy
Organism Homo sapiens
Characteristics disease state: Diffuse large B cell lymphoma (DLBCL)
specimen: Non-relapsing DLBCL primary
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_case36_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 May 06, 2016
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 GPL10123
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
23 0.040818002
24 -0.05857577
25 0.08647992
26 0.07610963
27 0.39713743
28 -0.41061783
29 -0.20564422
30 0.16145101
31 -0.030263862
32 7.67E-04
33 0.36515462
34 -0.36815172
35 0.28678492
36 -0.5361368
37 0.30051723
38 -0.008596037
39 0.098235935
40 -0.33778113
41 -0.029394392
42 0.17281935

Total number of rows: 173565

Table truncated, full table size 3035 Kbytes.




Supplementary file Size Download File type/resource
GSM2144372_pri_non_rel_case16.txt.gz 18.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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