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Sample GSM2208983 Query DataSets for GSM2208983
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 3 first treatment
Sample type genomic
 
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells CD19+
ighv mutational status: IgHV unmutated
tp53 diruption: no TP53 disruption detected
atm disruption: no ATM disruption detected
treatment: FC
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 AB 0.003225 AB 1242.613159 1273.546753
SNP_A-1967418 AB 0.005336 AB 475.216614 500.796692
SNP_A-1969580 BB 0.002831 BB 968.401489 2991.905518
SNP_A-4263484 AB 0.003218 AB 1926.379272 1325.340820
SNP_A-1978185 AA 0.001961 AA 1850.052979 473.022369
SNP_A-4264431 AA 0.006624 AA 1581.967773 465.216705
SNP_A-1980898 AB 0.000500 AB 912.482849 755.809143
SNP_A-1983139 AA 0.002832 AA 1992.399536 791.687012
SNP_A-4265735 AA 0.004008 AA 986.217102 387.478943
SNP_A-1995832 BB 0.002417 BB 645.404236 1353.945923
SNP_A-1995893 BB 0.001838 BB 513.251709 2201.476318
SNP_A-1997689 BB 0.002809 BB 738.244873 3208.670166
SNP_A-1997709 AA 0.000829 AA 1518.849243 327.043610
SNP_A-1997896 AA 0.006422 AA 1393.261353 770.196533
SNP_A-1997922 BB 0.002116 BB 659.920654 1290.721924
SNP_A-2000230 AA 0.034867 AA 2458.196289 1348.500122
SNP_A-2000332 AB 0.003794 AB 2100.918701 1947.265625
SNP_A-2000337 AA 0.001679 AA 1400.991943 407.639465
SNP_A-2000342 AA 0.004534 AA 3069.108398 1224.883911
SNP_A-4268173 AA 0.001519 AA 1431.103882 356.308044

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM2208983_CLL003_first_treatment.CEL.gz 28.2 Mb (ftp)(http) CEL
GSM2208983_CLL003_first_treatment.chp.gz 12.9 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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