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Sample GSM2208980 Query DataSets for GSM2208980
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 2 first treatment
Sample type genomic
 
Source name peripherel blood
Organism Homo sapiens
Characteristics cell type: mononuclear cells CD19+
ighv mutational status: IgHV mutated
tp53 diruption: no TP53 disruption detected
atm disruption: no ATM disruption detected
treatment: FC
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 0.000319 BB 775.974915 2417.224121
SNP_A-1967418 BB 0.004317 BB 400.780548 821.374329
SNP_A-1969580 BB 0.003165 BB 995.871704 3099.756836
SNP_A-4263484 BB 0.003285 BB 529.692017 1728.920410
SNP_A-1978185 AA 0.004459 AA 1501.591919 406.031860
SNP_A-4264431 AA 0.002921 AA 1650.106323 392.065094
SNP_A-1980898 BB 0.002918 BB 296.102142 875.896301
SNP_A-1983139 AA 0.003201 AA 2377.016113 791.620667
SNP_A-4265735 AA 0.007313 AA 1503.210327 434.112793
SNP_A-1995832 AB 0.005107 AB 1073.197754 846.075378
SNP_A-1995893 AB 0.003441 AB 1325.469360 1627.435547
SNP_A-1997689 BB 0.002134 BB 758.034302 3203.106445
SNP_A-1997709 AA 0.014991 AA 2220.689941 390.338989
SNP_A-1997896 AA 0.002097 AA 1428.331055 586.515259
SNP_A-1997922 AB 0.006355 AB 796.605103 705.070435
SNP_A-2000230 AA 0.007656 AA 3051.903320 1446.306885
SNP_A-2000332 AA 0.014916 AA 3366.874512 1107.547241
SNP_A-2000337 AA 0.004452 AA 1485.358032 326.451324
SNP_A-2000342 AA 0.002077 AA 3288.575928 997.518555
SNP_A-4268173 AA 0.004837 AA 1788.493286 326.451324

Total number of rows: 909622

Table truncated, full table size 46149 Kbytes.




Supplementary file Size Download File type/resource
GSM2208980_CLL002_first_treatment.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM2208980_CLL002_first_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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