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Sample GSM1056063 Query DataSets for GSM1056063
Status Public on Dec 21, 2013
Title ALL_Presentation_of_Patient_L173_Sty_Array
Sample type genomic
 
Source name bone marrow
Organism Homo sapiens
Characteristics disease stage: Presentation
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from bone marrow aspirates using the Qiagen DNAeasy blood and tissue kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel eletrophoresis.
Label biotin
Label protocol DNA was labelled according to the standard Affymetrix protocol for the Affymetrix GeneChip Human Mapping 500K Array Set.
 
Hybridization protocol Labelled DNA was hybridised according to manufacturer’s protocol.
Scan protocol Arrays were scanned according to manufacturer’s protocol.
Data processing The microarray data was processed using Affymetrix Genotyping Console (GTC) v4.0 to determine data quality. Genotype data was checked using the Concordance Check function within GTC to ensure no sampling errors had occurred during array processing. Copy number alterations were determined for 10 patients using the paired remission sample and the Hapmap894 reference 5 set within Partek Genomics Suite v6.5 (Partek, USA) as the reference for the remaining sample (L625). Further analysis, visualization and identification of genomic gains and losses were performed using Partek Genomics Suite v6.5 (Partek, USA) and SNPView2 v2.6 (Ilixa, UK). Regions of aberration were mapped according to the human reference sequence GRCh37.
 
Submission date Dec 20, 2012
Last update date Dec 21, 2013
Contact name Vikki Rand
E-mail(s) vikki.rand@newcastle.ac.uk
Organization name Newcastle University
Department Northern Institute for Cancer Research
Lab Lymphoma Genomics
Street address Paul O'Gorman Building, Newcastle University
City Newcastle Upon Tyne
State/province Tyne and Wear
ZIP/Postal code NE12 4HH
Country United Kingdom
 
Platform ID GPL3720
Series (1)
GSE43060 Genomic analysis of relapsed Acute Lymphoblastic Leukaemia in children

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 BB 0.003354 BB -0.783950 10.860218
AFFX-2315061 BB 0.019984 BB -0.865125 10.754569
AFFX-2315062 BB 0.009137 BB -0.549776 8.868502
AFFX-2315057 AB 0.018555 AB 0.016083 9.439870
AFFX-2315058 AA 0.018313 AA 0.738662 11.054038
AFFX-2315059 AB 0.014491 AB 0.178275 9.775775
AFFX-2315063 AA 0.035106 AA 0.571685 8.677626
AFFX-2315064 AA 0.044832 AA 0.718543 9.066322
AFFX-2315065 AA 0.153126 AA 0.382356 9.078178
AFFX-2315066 BB 0.023096 BB -0.503452 8.886958
AFFX-2315067 BB 0.004335 BB -0.456390 9.830128
AFFX-2315068 AB 0.000684 AB 0.106909 9.795753
AFFX-2315069 AB 0.080912 AB -0.001948 8.379906
AFFX-2315070 NC 0.667260 AA 0.263622 9.019946
AFFX-2315071 AB 0.085257 AB -0.174008 8.256186
AFFX-2315072 AB 0.313096 AB 0.206434 9.175524
AFFX-2315073 BB 0.039093 BB -0.485557 8.621211
AFFX-2315074 BB 0.037399 BB -0.712108 9.166665
AFFX-2315075 AA 0.012859 AA 0.696238 10.182878
AFFX-2315076 AB 0.017815 AB 0.053970 9.628589

Total number of rows: 238354

Table truncated, full table size 11099 Kbytes.




Supplementary file Size Download File type/resource
GSM1056063_S1233_STY_160807.CEL.gz 24.5 Mb (ftp)(http) CEL
GSM1056063_S1233_STY_160807.brlmm.chp.gz 3.9 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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