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Sample GSM2208988 Query DataSets for GSM2208988
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 5 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: ATMmut
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 0.003001 BB 591.456360 1914.772339
SNP_A-1967418 BB 0.004749 BB 289.700958 695.103149
SNP_A-1969580 BB 0.002120 BB 917.668335 2627.937012
SNP_A-4263484 AB 0.015820 AB 1923.422607 1665.814453
SNP_A-1978185 AA 0.007314 AA 2371.533447 597.770813
SNP_A-4264431 AA 0.005237 AA 1550.058350 414.202972
SNP_A-1980898 BB 0.000976 BB 316.243378 973.535767
SNP_A-1983139 AA 0.003262 AA 2364.866211 833.604736
SNP_A-4265735 AA 0.005405 AA 1320.839722 368.736206
SNP_A-1995832 NC 0.260730 BB 825.163391 1089.520020
SNP_A-1995893 BB 0.002280 BB 499.255341 2542.541260
SNP_A-1997689 BB 0.001424 BB 911.771118 3344.579590
SNP_A-1997709 AA 0.002737 AA 1750.818115 339.565308
SNP_A-1997896 AB 0.005083 AB 1138.301514 1846.812134
SNP_A-1997922 AB 0.002102 AB 1073.242798 1017.261902
SNP_A-2000230 NC 0.735819 AA 2522.778809 1911.214111
SNP_A-2000332 NC 0.136942 AA 2682.092529 1774.398315
SNP_A-2000337 AA 0.002648 AA 1428.525635 346.198029
SNP_A-2000342 AA 0.005409 AA 3205.317871 1260.998169
SNP_A-4268173 AA 0.002628 AA 1287.499023 300.490479

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM2208988_CLL005_pre_treatment.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM2208988_CLL005_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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