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Sample GSM2208994 Query DataSets for GSM2208994
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 8 pre treatment
Sample type genomic
 
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells
ighv mutational status: IgHV mutated
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 AB 0.005885 AB 1173.004150 954.727844
SNP_A-1967418 AB 0.015946 AB 910.532104 764.671143
SNP_A-1969580 BB 0.016899 BB 1223.152344 2740.155273
SNP_A-4263484 AB 0.007184 AB 1932.030640 1191.167358
SNP_A-1978185 AA 0.019693 AA 2669.515625 599.874878
SNP_A-4264431 AA 0.007274 AA 2093.931885 334.884918
SNP_A-1980898 BB 0.001648 BB 283.840607 1039.313843
SNP_A-1983139 AA 0.004939 AA 1477.172852 567.610718
SNP_A-4265735 AB 0.000788 AB 850.894775 914.255676
SNP_A-1995832 AB 0.008292 AB 1432.186890 1319.541504
SNP_A-1995893 BB 0.008290 BB 524.612427 2923.667969
SNP_A-1997689 BB 0.000802 BB 790.649109 3144.307861
SNP_A-1997709 AA 0.008427 AA 1129.264526 266.239624
SNP_A-1997896 AB 0.001195 AB 1307.700439 1806.428833
SNP_A-1997922 AB 0.011610 AB 1146.551636 1250.043579
SNP_A-2000230 AB 0.091464 AB 2234.298096 2056.968506
SNP_A-2000332 AA 0.044524 AA 2592.185303 1638.250000
SNP_A-2000337 AA 0.010873 AA 1053.543335 511.728210
SNP_A-2000342 AA 0.001516 AA 3297.911621 1108.324951
SNP_A-4268173 AA 0.001359 AA 1550.332886 320.251770

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM2208994_CLL008_pre_treatment.CEL.gz 27.3 Mb (ftp)(http) CEL
GSM2208994_CLL008_pre_treatment.chp.gz 12.7 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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