NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6986361 Query DataSets for GSM6986361
Status Public on Aug 05, 2023
Title genomic DNA from Muskrat Liver 203203210077_R02C02
Sample type genomic
 
Source name Liver
Organism Ondatra zibethicus
Characteristics age: NA
confidenceinageestimate: NA
female: NA
speciescommonname: Muskrat
maximumlifespanyears: 10
average_adultweight: 1362
ageatsexualmaturityyears: 0.780821917808219
networktrainingset: yes
panmammalianclocktrainingset: no
Extracted molecule genomic DNA
Extraction protocol none provided
Label Cy5
Label protocol standard Affymetrix protocol
 
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 Muskrat 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 05, 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
GSM6986361_203203210077_R02C02_Grn.idat.gz 384.1 Kb (ftp)(http) IDAT
GSM6986361_203203210077_R02C02_Red.idat.gz 385.0 Kb (ftp)(http) IDAT
Processed data are available on Series record

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