NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6979785 Query DataSets for GSM6979785
Status Public on Aug 05, 2023
Title genomic DNA from Mouse Liver 202894750021_R01C01
Sample type genomic
 
Source name Liver
Organism Mus musculus
Characteristics age: 0.833333333
confidenceinageestimate: 100
female: 0
speciescommonname: Mouse
maximumlifespanyears: 4
average_adultweight: 20.5
ageatsexualmaturityyears: 0.115068493150685
networktrainingset: yes
panmammalianclocktrainingset: yes
experiment: Genetic perturbation
intervention: WT
Extracted molecule genomic DNA
Extraction protocol none provided
Label Cy5
Label protocol Zymo EZ DNA Methylation Kit
 
Hybridization protocol standard protocols from Illumina regarding Infinium arrays
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description genomic DNA from Mouse Liver
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.
normalized (Sesame) Beta values
 
Submission date Jan 25, 2023
Last update date Aug 18, 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 GPL28271
Series (1)
GSE223748 Mammalian Methylation Consortium

Supplementary file Size Download File type/resource
GSM6979785_202894750021_R01C01_Grn.idat.gz 384.0 Kb (ftp)(http) IDAT
GSM6979785_202894750021_R01C01_Red.idat.gz 384.3 Kb (ftp)(http) IDAT
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap