|
Status |
Public on Aug 05, 2024 |
Title |
G703E_7T77_1_V1_Epigenetics |
Sample type |
genomic |
|
|
Source name |
Blood
|
Organism |
Homo sapiens |
Characteristics |
Sex: Male race: African ethnicity: Mandinka tissue: Blood cell type: Whole blood treatment: HBV D3
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Extration method used the Chemagic low volume blood kit, Bead based, Chemagic DNA 400 kit H96 (Cat# CMG-1491), where 1.5ug DNA was extracted from whole blood and send to AGRF Genotyping Service.
|
Label |
Cy3 and Cy5
|
Label protocol |
standard Illumina Protocol
|
|
|
Hybridization protocol |
Samples were normalised to ~250ng DNA in 45uL and bisulfite converted using Zymo EZ-96 DNA Methylation Kit.. Used Illumina Human Methylation EPIC BeadChip following the Illumina Infinium HD Methylation Assay
|
Scan protocol |
Arrays were imaged using BeadArray Reader (HiScan) and the standard recommended Illumina scanner setting.
|
Data processing |
Raw .idat files were read into an R statistical environment using the minfi package. Using the minfi package in R, Sample QC was performed, and failed samples were removed from analysis. Probe level QC was performed, and poorly performing probes and known blacklist probes were removed.
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|
|
Submission date |
Jul 22, 2024 |
Last update date |
Aug 05, 2024 |
Contact name |
Ofer Levy |
E-mail(s) |
meagan.karoly@childrens.harvard.edu, ofer.levy@childrens.harvard.edu, Joann.Arce@childrens.harvard.edu
|
Phone |
617-919-2904
|
Organization name |
Boston Children's Hospital
|
Department |
Infectious Disease
|
Lab |
Levy Lab
|
Street address |
300 Longwood Avenue
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02115 |
Country |
USA |
|
|
Platform ID |
GPL21145 |
Series (1) |
GSE272800 |
Systems Biology to Identify Biomarkers of Neonatal Vaccine Immunogenicity [methylation] |
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