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Status |
Public on Feb 12, 2016 |
Title |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131146_R01C02] |
Sample type |
genomic |
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Source name |
Reconstructed mixture of purified human leukocytes
|
Organism |
Homo sapiens |
Characteristics |
cd4+ t cell (%): 9 cd8+ t cell (%): 6 b cell (%): 2 natural killer cell (%): 0 monocyte (%): 10 granulocyte (%): 73
|
Treatment protocol |
Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec; venous whole blood was collected into Heparin
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted using QIAGEN Dneasy blood and tissue kit according to standard instructions
|
Label |
Cy5 and Cy3
|
Label protocol |
Standard Illumina Protocol
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Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
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Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
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Description |
X9985131146_R01C02 DNA methylation profiling across mixture of white blood cell (WBC) types SAMPLE 9
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Data processing |
Unmethylated and methylated signal intensities were generated using the publicly available, minfi Bioconductor package. Data processing of these data was also carried out using the minfi Bioconductor package and included: background subtraction and normalization utilizing the various internal controls present on the Illumina Infinium Methylation450 BeadChip and Subset quantile within array-normalization (SWAN) to adjust the beta-values of type 2 design probes into a statistical distribution characteristic of type 1 probes.
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Submission date |
Feb 10, 2016 |
Last update date |
Feb 12, 2016 |
Contact name |
Devin Charles Koestler |
E-mail(s) |
dkoestler@kumc.edu
|
Phone |
9135884788
|
Organization name |
University of Kansas Medical Center
|
Department |
Biostatistics
|
Street address |
3901 Rainbow Blvd.
|
City |
Kansas City |
State/province |
KS |
ZIP/Postal code |
66160 |
Country |
USA |
|
|
Platform ID |
GPL13534 |
Series (1) |
GSE77797 |
DNA methylation profiling of whole blood and reconstructed mixtures of purified leukocytes isolated from human adult blood |
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