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Sample GSM7008120 Query DataSets for GSM7008120
Status Public on Aug 07, 2023
Title P31.Dataset, 206535570002_R06C02
Sample type genomic
 
Source name 206535570002_R06C02
Organism Mus musculus
Characteristics age: 0.498630137
confidenceinageestimate: 100
tissue: Liver
female: 0
tissuedetailed: Liver
age.1: 1/0/1900
specieslatinname: Mus musculus
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted
Label Cy3 and Cy5
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridized to the the Beadchip HorvathMammalMethylChip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Data processing Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs. Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/ A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.
 
Submission date Jan 28, 2023
Last update date Aug 07, 2023
Contact name Steve Horvath
E-mail(s) shorvath@altoslabs.com
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Platform ID GPL32543
Series (1)
GSE223944 P31.Dataset

Data table header descriptions
ID_REF
VALUE normalized (Sesame) Beta values

Data table
ID_REF VALUE
cg00000165_TC21 0.539197745320669
cg00001209_TC21 0.907753572224809
cg00001364_TC21 0.916444823109093
cg00001582_TC21 0.0463505062521325
cg00002920_TC21 0.727645138270755
cg00003994_TC21 0.0373616651999016
cg00004555_BC21 0.0649414543017352
cg00005112_TC21 0.882981983778769
cg00005271_TC21 0.962044891251988
cg00006213_TC21 0.870612763575079
cg00008998_TC21 0.479946526448995
cg00009248_TC21 0.85906810832813
cg00009319_BC21 0.330448287964152
cg00010445_TC21 0.762968363392449
cg00010903_BC21 0.52076116199915
cg00010926_BC21 0.928044978886129
cg00010977_TC21 0.896773130315978
cg00012521_TO21 0.53045239392158
cg00012879_TC21 0.496366564393757
cg00013189_BC11 0.0207533732032938

Total number of rows: 326732

Table truncated, full table size 10863 Kbytes.




Supplementary file Size Download File type/resource
GSM7008120_206535570002_R06C02_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008120_206535570002_R06C02_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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