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Sample GSM4230830 Query DataSets for GSM4230830
Status Public on Mar 09, 2020
Title subject ID 33007-0 at diease time point 4_Male, a T1D case and 3.2416153yrs old_450K array [3998909132_R04C02]
Sample type genomic
 
Source name T1D case_Male_time point 4
Organism Homo sapiens
Characteristics subject id: 33007-0
disease time point: 4
age: 3.241615332
Sex: Male
t1d status: T1D case
tissue: peripheral blood sample
Extracted molecule genomic DNA
Extraction protocol Standard Illumina Protocol
Label cy3, cy5
Label protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human450K or EPIC Beadchip using standard Illumina protocol
 
Hybridization protocol Standard Illumina Protocol
Scan protocol Standard Illumina Protocol
Data processing SeSAMe (v1.0.0) pipeline was used to normalize data (via Noob), perform dye bias correction and perform probe specific QC (via pOOBAH).
ComBat was used to adjust for batch effects were batch was considered to be plate and row position combination
Filtered probes with a small Beta range (range < 0.05), those with known SNPs in the CpG site, and those located on the sex chromosomes
Mvalues.normalized.*.txt contains methylation M-value
 
Submission date Dec 22, 2019
Last update date Mar 09, 2020
Contact name Lauren Vanderlinden
E-mail(s) lauren.vanderlinden@cuanschutz.edu
Organization name Colorado School of Public Health
Department Department of Biostatistics and Informatics
Street address 13001 E. 17th Place, Mail Stop B119
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
 
Platform ID GPL13534
Series (1)
GSE142512 Longitudinal DNA methylation differences precede type 1 diabetes

Supplementary file Size Download File type/resource
GSM4230830_3998909132_R04C02_Grn.idat.gz 4.2 Mb (ftp)(http) IDAT
GSM4230830_3998909132_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data are available on Series record

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