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| Status |
Public on Jun 04, 2020 |
| Title |
00d1_4cde-PBMC |
| Sample type |
genomic |
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| Source name |
Human PBMCs at age 7
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMCs
age: age 7
methylationplatenumber: 1
selfreportedrace: Black
gestationalage_birth: 39
Sex: Male
samplecollectionsite: Baltimore
ancestry_pc1: 12.47110081
ancestry_pc2: 1.474864502
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA for methylation studies was extracted from thawed CBMCs and PBMCs using the Qiagen AllPrep kit (QIAGEN, Valencia, CA)
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| Label |
Cy3, Cy5
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| Label protocol |
Illumina Infinium
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| Hybridization protocol |
Illumina Infinium
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| Scan protocol |
Illumina IScan
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| Description |
Sample 00d1_4cde, age 7
Measured on EPIC array
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| Data processing |
1.) Remove probes with SNPs whose MAF is >= 0.05 in Africans, Americans or Europeans. 2.) Remove cross hybridizing probes; remove probes on sex chromosomes; remove probes with a detection pvalue >= 0.01 in more than 25% of the samples. 3.) Samples 7804_4bab-CBMC, a60f_493d-CBMC, f86d_4016-PBMC failed QC and were removed from downstream analysis. 4.) Normalize methylated and unmethylated probe intensities separately with normalize.quantile.450k(<Methylset_Object>, method = "quantile1"); this is from ENmix package, version 1.14.0. 5.) Remove probe-type bias with preprocessSWAN from the minfi package, version 1.24.0. 6.) Calculate M-values as log2(Processed unmethylated intensity + 100) - log2(Processed methylated intensity + 100). M-values were used in all downstream analyses.
Normalized Beta-value, calculated as (Normalized methylated intensity + 100)/{(Normalized methylated intensity + 100) + (Normalized unmethylated intensity + 100)}. The offset of 100 was recommended by Du et al., 2010
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| Submission date |
Jun 04, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Carole Ober |
| E-mail(s) |
c-ober@genetics.uchicago.edu
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| Organization name |
The University of Chicago
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| Department |
Human Genetics
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| Lab |
Ober
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| Street address |
920 E 58TH ST
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL21145 |
| Series (1) |
| GSE132181 |
Genome wide blood DNA methylation measured at birth and age 7 on the EPIC array |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM3852272_200673760041_R08C01_Grn.idat.gz |
7.0 Mb |
(ftp)(http) |
IDAT |
| GSM3852272_200673760041_R08C01_Red.idat.gz |
7.0 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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