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Sample GSM2208978 Query DataSets for GSM2208978
Status Public on Aug 25, 2017
Title Chronic lymphocytic leukemia 1 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 0.028798 BB 1399.146973 2724.762695
SNP_A-1967418 AB 0.008990 AB 813.445740 657.263611
SNP_A-1969580 BB 0.004464 BB 924.913086 2326.609863
SNP_A-4263484 AA 0.023649 AA 1818.666016 526.426941
SNP_A-1978185 AA 0.000775 AA 1929.930908 526.426941
SNP_A-4264431 AA 0.010410 AA 1629.998169 532.031860
SNP_A-1980898 BB 0.015700 BB 364.025604 738.786865
SNP_A-1983139 AA 0.001837 AA 1746.398926 666.636047
SNP_A-4265735 AB 0.006409 AB 1259.726318 1282.284912
SNP_A-1995832 BB 0.007860 BB 653.497620 1851.942871
SNP_A-1995893 BB 0.003141 BB 581.513000 2205.989990
SNP_A-1997689 BB 0.032358 BB 1201.309937 2883.347412
SNP_A-1997709 AA 0.015761 AA 1384.613037 425.974243
SNP_A-1997896 AB 0.008286 AB 948.988831 1293.943481
SNP_A-1997922 AA 0.004430 AA 1087.678589 395.763824
SNP_A-2000230 AA 0.027209 AA 3742.435547 1819.285889
SNP_A-2000332 AA 0.009825 AA 3094.894287 950.982727
SNP_A-2000337 AA 0.010370 AA 1285.521362 524.562927
SNP_A-2000342 AA 0.021747 AA 3294.633057 1444.029541
SNP_A-4268173 BB 0.001569 BB 388.040192 1619.262939

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM2208978_CLL001_paired_normal.CEL.gz 27.3 Mb (ftp)(http) CEL
GSM2208978_CLL001_paired_normal.chp.gz 12.8 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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