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Sample GSM2208992 Query DataSets for GSM2208992
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 7 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
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 0.010806 BB 585.734863 1594.444092
SNP_A-1967418 BB 0.011056 BB 312.636993 980.443298
SNP_A-1969580 BB 0.007860 BB 1190.272827 2833.303955
SNP_A-4263484 AB 0.016396 AB 2281.345947 1674.169067
SNP_A-1978185 AA 0.007717 AA 2033.526367 700.174561
SNP_A-4264431 AA 0.001924 AA 2048.841064 421.333038
SNP_A-1980898 AB 0.002779 AB 1010.066528 727.024231
SNP_A-1983139 AA 0.008844 AA 2128.365967 898.444885
SNP_A-4265735 BB 0.005383 BB 588.975769 1455.351685
SNP_A-1995832 AB 0.000367 AB 1350.674561 1016.727356
SNP_A-1995893 AB 0.022860 AB 1139.688599 2567.753662
SNP_A-1997689 BB 0.000936 BB 774.783264 3095.161377
SNP_A-1997709 AA 0.003563 AA 1365.735596 347.250641
SNP_A-1997896 AB 0.005318 AB 1388.515015 2073.947021
SNP_A-1997922 AA 0.006299 AA 1606.811890 427.306702
SNP_A-2000230 AA 0.011824 AA 3013.533447 1582.318604
SNP_A-2000332 AB 0.004136 AB 2529.539062 2530.595215
SNP_A-2000337 AA 0.003697 AA 1116.862671 387.784393
SNP_A-2000342 AA 0.005393 AA 3610.060303 1131.526245
SNP_A-4268173 AA 0.007208 AA 2044.192627 496.301544

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM2208992_CLL007_pre_treatment.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM2208992_CLL007_pre_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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