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Sample GSM2208982 Query DataSets for GSM2208982
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 3 pre treatment
Sample type genomic
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells
ighv mutational status: IgHV unmutated
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
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

Data table
SNP_A-2131660 AB 0.010134 AB 989.374512 942.084045
SNP_A-1967418 AB 0.000463 AB 631.562805 575.804077
SNP_A-1969580 BB 0.003866 BB 1193.684082 3392.506104
SNP_A-4263484 AB 0.006937 AB 1966.151367 1532.994995
SNP_A-1978185 AA 0.002483 AA 1918.219727 479.491974
SNP_A-4264431 AA 0.003532 AA 2189.751953 485.747925
SNP_A-1980898 AB 0.004370 AB 1075.710571 876.619324
SNP_A-1983139 AA 0.002171 AA 2117.108643 688.580444
SNP_A-4265735 AA 0.003108 AA 1067.380493 335.203400
SNP_A-1995832 BB 0.008409 BB 644.661194 1138.178589
SNP_A-1995893 BB 0.000577 BB 533.340210 2324.051270
SNP_A-1997689 BB 0.006082 BB 641.867920 3156.682861
SNP_A-1997709 AA 0.000942 AA 1623.090820 335.203400
SNP_A-1997896 AA 0.010040 AA 2230.300293 690.246338
SNP_A-1997922 BB 0.008285 BB 615.355530 1635.508301
SNP_A-2000230 AA 0.037071 AA 2215.648682 1078.108521
SNP_A-2000332 AB 0.003146 AB 2474.043945 2453.705078
SNP_A-2000337 AA 0.004173 AA 1138.178589 356.602936
SNP_A-2000342 AA 0.004003 AA 3525.817139 1096.945923
SNP_A-4268173 AA 0.002596 AA 1698.215576 335.203400

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.

Supplementary file Size Download File type/resource
GSM2208982_CLL003_pre_treatment.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM2208982_CLL003_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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