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Sample GSM1059807 Query DataSets for GSM1059807
Status Public on Jan 04, 2013
Title DLBCL cell line K422 versus male control DNA
Sample type genomic
 
Channel 1
Source name DLBCL cell line K422
Organism Homo sapiens
Characteristics gender: female
cell line: DLBCL cell line K422
cell type: diffuse large B-cell lymphoma (DLBCL)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from DLBCL cell lines was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's recommendations.
Label Cy5
Label protocol NimbleGen Labeling Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/labeling/index.html)
 
Channel 2
Source name male control DNA
Organism Homo sapiens
Characteristics gender: male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from DLBCL cell lines was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer's recommendations.
Label Cy3
Label protocol NimbleGen Labeling Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/labeling/index.html)
 
 
Hybridization protocol NimbleGen Hybridization Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/kits/hybridization/index.html)
Scan protocol NimbleGen Scan Protocol (Proprietary protocol information available at http://www.nimblegen.com/products/software/nimblescan/index.html)
Description K422 vs maleControlDNA
Data processing The unspecific binding intensity was estimated using the random control probes and subtracted. Outlier probes and probes with too low signal were detected and removed (set to NaN). [Note: (1) the two 'DNAPool vs maleControlDNA' replicates were averaged already on signal level to get more robust results (thus the processed log2(ratio)s for these two replicates are identical). (2) The normalized values of the random sequence probes (e.g. RANDOM00000001, RANDOM00000002 etc) were used to subtract the unspecific binding offsets and included in the full_normalized_data.txt file available on Series records.]
 
Submission date Jan 03, 2013
Last update date Jan 04, 2013
Contact name Michael Grau
Organization name University of Münster
Department Faculty of Medicine
Lab Translational Oncology
Street address Albert-Schweitzer-Campus 1
City Münster
State/province Nordrhein-Westfalen
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL15436
Series (1)
GSE43272 MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma

Data table header descriptions
ID_REF
VALUE log2(ratio)s, i.e. -log2(linear signal of REF/Cy3 channel) + log2(linear signal of EXP/Cy5 channel)

Data table
ID_REF VALUE
CHR01FS000032108 0.009415627
CHR01FS000036566 -0.4501791
CHR01FS000037196 -0.284014702
CHR01FS000038109 -0.345674515
CHR01FS000039532 -0.383318901
CHR01FS000049283 -0.234209061
CHR01FS000052308 0.111616135
CHR01FS000055650 -0.042780876
CHR01FS000059489 -0.383331299
CHR01FS000060884 -0.300509453
CHR01FS000072260 -0.375626564
CHR01FS000241735 -0.217687607
CHR01FS000357503 -0.368920326
CHR01FS000389471 0.083805084
CHR01FS000403676 -0.301671982
CHR01FS000443361 0.038039207
CHR01FS000530358 -0.183660507
CHR01FS000532718 -0.263053894
CHR01FS000547649 -0.682823181
CHR01FS000553694 -0.277783394

Total number of rows: 719690

Table truncated, full table size 20503 Kbytes.




Supplementary file Size Download File type/resource
GSM1059807_439549A02_532.pair.gz 12.4 Mb (ftp)(http) PAIR
GSM1059807_439549A02_635.pair.gz 12.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data are available on Series record

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