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Sample GSM2208981 Query DataSets for GSM2208981
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 2 paired normal
Sample type genomic
 
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells CD19-
ighv mutational status: not annotated
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 0.003602 BB 646.649475 1883.974976
SNP_A-1967418 BB 0.001348 BB 330.256561 753.807556
SNP_A-1969580 BB 0.001456 BB 988.430176 2656.610107
SNP_A-4263484 BB 0.002528 BB 602.524170 1685.139526
SNP_A-1978185 AA 0.005568 AA 1653.024170 378.758636
SNP_A-4264431 AA 0.006570 AA 1465.106323 333.612946
SNP_A-1980898 BB 0.000717 BB 301.267273 1017.595398
SNP_A-1983139 AA 0.009036 AA 2539.405029 965.807861
SNP_A-4265735 AA 0.001516 AA 1409.388184 504.182465
SNP_A-1995832 AB 0.001617 AB 1478.527222 1038.720337
SNP_A-1995893 AB 0.002552 AB 1354.801880 1683.786743
SNP_A-1997689 BB 0.003993 BB 789.980713 2757.354736
SNP_A-1997709 AA 0.003906 AA 1756.419312 325.839294
SNP_A-1997896 AA 0.001326 AA 1651.074219 707.543030
SNP_A-1997922 AB 0.005290 AB 777.401001 815.920288
SNP_A-2000230 AA 0.026389 AA 2577.439453 1401.928589
SNP_A-2000332 AA 0.005374 AA 2986.934570 1041.011597
SNP_A-2000337 AA 0.008568 AA 1610.320801 305.988403
SNP_A-2000342 AA 0.007372 AA 3392.508301 1300.817993
SNP_A-4268173 AA 0.005916 AA 1882.598145 491.937897

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.




Supplementary file Size Download File type/resource
GSM2208981_CLL002_paired_normal.CEL.gz 28.2 Mb (ftp)(http) CEL
GSM2208981_CLL002_paired_normal.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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