NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8412711 Query DataSets for GSM8412711
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.
 
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]

Supplementary file Size Download File type/resource
GSM8412711_204936500122_R05C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM8412711_204936500122_R05C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.