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| Status |
Public on Nov 24, 2014 |
| Title |
100082_peripheral_CD14 [methylation] |
| Sample type |
genomic |
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| Source name |
CD14+ cell
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| Organism |
Homo sapiens |
| Characteristics |
ChIP: 5854945036
well: R05C02
age: 78
racegendersite: 2
bcell: 0.141864564
tcell: 0.003467707
nkcell: 0.222282403
neutro: 0.250452221
plaque: 0
cac: 908.52
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| Treatment protocol |
Not applicable
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| Growth protocol |
Not applicable
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Blood was initially collected in sodium heparin-containing Vacutainer CPTTM cell separation tubes (Becton Dickinson, Rutherford, NJ) to separate peripheral blood mononuclear cells from other elements within 2 hours from blood draw. Subsequently, monocytes were isolated with the anti-CD14 coated magnetic beads, respectively, using AutoMACs automated magnetic separation unit (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA and RNA were isolated from samples simultaneously using the AllPrep DNA/RNA Mini Kit (Qiagen, Inc., Hilden, Germany).
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| Label |
Cy5 and Cy3
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| Label protocol |
The Illumina HumanMethylation450 BeadChip and HiScan reader were used to perform the epigenome-wide methylation analysis. The EZ-96 DNA MethylationTM Kit (Zymo Research, Orange, CA) was used for bisulfate conversation with 1ug of input DNA (at 45 ul). 4 ul of bisulfite-converted DNA were used for DNA methylation assays, following the Illumina Infinium HD Methylation protocol. This consisted of a whole genome amplification step followed by enzymatic end-point fragmentation, precipitation, and resuspension.
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| Hybridization protocol |
The resuspended samples were hybridized on HumanMethylation 450 BeadChips at 48°C for 16 h.
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| Scan protocol |
Illumina HiScan reader
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| Description |
human peripheral CD14+ cells
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| Data processing |
Bead-level methylation data were summarized in GenomeStudio. Because a two-channel system and both Infinium I and II assays were used, normalization was performed in several steps using the lumi package (27). We first adjusted for color bias using “smooth quantile normalization”. Next, the data were background adjusted by subtracting the median intensity value of the negative control probes. Lastly, data were normalized across all samples by standard quantile normalization applied to the bead-type intensities and combined across Infinium I and II assays and both colors.
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| Submission date |
Mar 19, 2014 |
| Last update date |
May 11, 2018 |
| Contact name |
Yongmei Liu |
| E-mail(s) |
yoliu@wakehealth.edu
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| Organization name |
Wake Forest School of Medicine
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| Street address |
Medical Center Blvd.
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| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27157 |
| Country |
USA |
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| Platform ID |
GPL13534 |
| Series (2) |
| GSE56046 |
Transcriptomics and methylomics of human monocytes [methylome] |
| GSE56047 |
Transcriptomics and methylomics of human monocytes |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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