|
| Status |
Public on Feb 12, 2016 |
| Title |
Genomic DNA from a reconstructed mixture of purified human leukocytes [9985131137_R06C02] |
| Sample type |
genomic |
| |
|
| Source name |
Reconstructed mixture of purified human leukocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cd4+ t cell (%): 12
cd8+ t cell (%): 5
b cell (%): 6
natural killer cell (%): 7
monocyte (%): 4
granulocyte (%): 66
|
| 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
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
X9985131137_R06C02
DNA methylation profiling across mixture of white blood cell (WBC) types
SAMPLE 11
|
| 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.
|
| |
|
| 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 |
|
