NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7008081 Query DataSets for GSM7008081
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570058_R03C02
Sample type genomic
 
Source name 206535570058_R03C02
Organism Mus musculus
Characteristics age: 0.520547945
confidenceinageestimate: 100
tissue: Blood
female: 1
tissuedetailed: Blood
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)
GSE223943 P30.Dataset

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

Data table
ID_REF VALUE
cg00000165_TC21 0.494528661517674
cg00001209_TC21 0.924934133839963
cg00001364_TC21 0.965440458273726
cg00001582_TC21 0.0493346724854783
cg00002920_TC21 0.160768118323238
cg00003994_TC21 0.0260373154673071
cg00004555_BC21 0.128092847806374
cg00005112_TC21 0.945785583287247
cg00005271_TC21 0.965195036334982
cg00006213_TC21 0.931279801556387
cg00008998_TC21 0.487489446169106
cg00009248_TC21 0.941002657133903
cg00009319_BC21 0.450470825378684
cg00010445_TC21 0.880774487277471
cg00010903_BC21 0.493269018229204
cg00010926_BC21 0.912808051375732
cg00010977_TC21 0.929986873973658
cg00012521_TO21 0.51255109796399
cg00012879_TC21 0.545204065102653
cg00013189_BC11 0.0137614610036841

Total number of rows: 326732

Table truncated, full table size 10857 Kbytes.




Supplementary file Size Download File type/resource
GSM7008081_206535570058_R03C02_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008081_206535570058_R03C02_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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