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Sample GSM931261 Query DataSets for GSM931261
Status Public on Nov 26, 2012
Title H321
Sample type genomic
 
Source name Sample from patient with diffuse large B-cell lymphoma
Organism Homo sapiens
Characteristics tissue: sample of diffuse large B-cell lymphoma
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol The tumor sample was after removal snap frozen and stored in OCT at - 80 oC. From each OCT block, 3x20 µm cuts were obtained using a microtome; the slices were washed twice in PBS and homogenized using the TissueLyser II (Qiagen). DNA extraction was performed using the DNeasy Blood & Tissue kit (Qiagen). From one of the patients (H380) a peripheral blood sample was included as a normal control sample (BB39). Mononuclear cells were isolated from the blood sample by Ficoll-Paque Plus (GE Health Care, Uppsala, Sweden) and stored in 10 % DMSO and 20 % serum at – 80 oC. For DNA extraction, the cells were thawed, washed twice in PBS and genomic DNA extracted using the DNeasy Blood & Tissue kit (Qiagen). The DNA was eluted in water and the concentration measured using a Nanodrop (Thermo Scientific)
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to cytogenetic 2.7M whole-genome array
Data processing CEL files from the Cyto2.7M array were imported and analyzed using ChAS with default analysis parameter settings (file: Cytogenetics_Array.single_sample.def.NA31.chasparam), except for a change to regional GC correction to generate CYCHP-files, which were also viewed in ChAS. TXT files of normalized data were exported from the Chromosome Analysis Suite software. All genomic positions were annotated to the hg19 version of the human genome (NCBI build 37).
Detection of CNVs larger than 200 kb with size being the only restriction.
 
Submission date May 14, 2012
Last update date Nov 26, 2012
Contact name Julie Støve Bødker
E-mail(s) j.boedker@rn.dk
Organization name Aalborg University Hospital
Department Department of Heamatology
Lab Research Laboratory
Street address Sdr. Skovvej 15
City Aalborg
ZIP/Postal code 9000
Country Denmark
 
Platform ID GPL11157
Series (2)
GSE37978 Cyto2.7M copy number analysis of eight diffuse large B-cell samples and one matched blood sample
GSE37979 Performance Comparison of the Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-genome Microarrays in Complex Cancer Samples

Data table header descriptions
ID_REF
VALUE Log2Ratio
Chromosome
Position
WeightedLog2Ratio
SmoothSignal

Data table
ID_REF VALUE Chromosome Position WeightedLog2Ratio SmoothSignal
C-0HT3C -0.004132 1 712577 -0.004132 2.364387
C-0HT3D 0.25624 1 713263 -0.004132 2.363804
C-0HT3E 0.53267 1 714145 -0.004132 2.363849
C-0HT3F -0.371203 1 714635 0.130318 2.362666
C-0HT3I -0.022044 1 718604 0.130318 2.363008
C-0HT48 0.130318 1 750062 -0.022044 2.363031
C-0HT4C 0.429544 1 752757 -0.022044 2.363487
S-2K62M -0.169854 1 754192 0.130318 2.362806
C-0HT4G -0.092832 1 755354 0.209769 2.362993
C-0HT4K 0.209769 1 760401 0.041136 2.363195
C-0HT4L 0.349745 1 761332 0.069504 2.363784
C-0HT4M 0.041136 1 762116 0.209769 2.363704
C-0HT4O 0.069504 1 764909 0.317612 2.363818
C-0HT4P 0.317612 1 765399 0.317612 2.363959
C-0HT4R 0.442937 1 767604 0.440732 2.363823
S-2H4KY 0.598055 1 768448 0.440732 2.36385
C-0HT4U 0.440732 1 772945 0.440732 2.364275
S-2K3DK 0.250028 1 777122 0.400628 2.363062
C-0HT4X 0.400628 1 779315 0.271461 2.363366
S-2KEV0 0.271461 1 779322 0.250028 2.36338

Total number of rows: 2141361

Table truncated, full table size 98036 Kbytes.




Supplementary file Size Download File type/resource
GSM931261_H321_Cytogenetics_Array_.CEL.gz 20.4 Mb (ftp)(http) CEL
GSM931261_H321_Cytogenetics_Array_.cychp.gz 38.3 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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