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Sample GSM2208979 Query DataSets for GSM2208979
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 2 pre treatment
Sample type genomic
 
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells
ighv mutational status: IgHV mutated
tp53 diruption: no TP53 disruption detected
atm disruption: no ATM disruption detected
treatment: not annotated
best clinical response: not annotated
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations from peripheral blood using the Qiagen® DNA Blood Mini Kit (Hilden, Germany). Immunomagnetic tumor cell enrichment was performed for a subset of samples (Midi MACS, Miltenyi Biotec®; Bergisch Gladbach, Germany) so that 98 mononuclear cell fractions, 118 CD19-positive fractions, and 52 CD19-negative fractions were used. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
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 GenomeWide SNP 6.0 array
Data processing CEL-files and chp-files (generated by Affymetrix GTYPE using the DM algorithm and by the birdseed algorithm in Affymetrix Genotyping Console version 4.0, respectively) were processed by dChip and model-based expression performed using the PM/MM model.
Signal' = Summarized signal; Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
 
Submission date Jun 20, 2016
Last update date Aug 25, 2017
Contact name Jennifer Edelmann
E-mail(s) j.edelmann@qmul.ac.uk
Phone 0041 (0)20 7882 8780
Organization name Barts Cancer Institute
Department Centre for Haemato-/Oncology
Lab 3rd Floor John Vane Science Centre
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL6801
Series (1)
GSE83566 Frequent Evolution of Copy Number Alterations Following First‑line Treatment with FC(R) is Enriched with TP53 Alterations which Impact Long Term Survival – Results from the CLL8 Trial

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.007422 BB 658.822205 1749.271973
SNP_A-1967418 BB 0.006826 BB 268.988464 678.236145
SNP_A-1969580 BB 0.001708 BB 1043.477173 2744.077393
SNP_A-4263484 BB 0.001728 BB 743.588684 2055.953613
SNP_A-1978185 AA 0.004592 AA 2255.266357 595.498352
SNP_A-4264431 AA 0.002675 AA 1691.872925 424.600525
SNP_A-1980898 BB 0.001154 BB 291.501709 1025.822388
SNP_A-1983139 AA 0.003219 AA 1786.076782 735.377258
SNP_A-4265735 AA 0.001520 AA 1412.812134 508.074097
SNP_A-1995832 AB 0.004875 AB 1352.624878 802.242493
SNP_A-1995893 AB 0.006148 AB 1232.239990 2164.337402
SNP_A-1997689 BB 0.007089 BB 833.627563 3654.799072
SNP_A-1997709 AA 0.001316 AA 1473.869995 320.661072
SNP_A-1997896 AA 0.003119 AA 1526.465942 749.011475
SNP_A-1997922 AB 0.000890 AB 1032.316162 945.819702
SNP_A-2000230 NC 0.531167 AB 2248.239014 1832.554199
SNP_A-2000332 AA 0.004872 AA 2407.051758 1261.884033
SNP_A-2000337 AA 0.000885 AA 1258.409912 384.560577
SNP_A-2000342 AA 0.015720 AA 2873.535889 1322.510498
SNP_A-4268173 AA 0.001918 AA 1388.307495 349.286285

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM2208979_CLL002_pre_treatment.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM2208979_CLL002_pre_treatment.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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