NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7008076 Query DataSets for GSM7008076
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570058_R04C01
Sample type genomic
 
Source name 206535570058_R04C01
Organism Mus musculus
Characteristics age: 0.520547945
confidenceinageestimate: 100
tissue: Blood
female: 0
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 0.463717018404474
cg00001209_TC21 0.939428915439554
cg00001364_TC21 0.952120067862369
cg00001582_TC21 0.0546968746895857
cg00002920_TC21 0.143670216979306
cg00003994_TC21 0.0353128933362204
cg00004555_BC21 0.148897671856099
cg00005112_TC21 0.951265236854494
cg00005271_TC21 0.966896430003627
cg00006213_TC21 0.926178735221347
cg00008998_TC21 0.512400608860108
cg00009248_TC21 0.953676391804047
cg00009319_BC21 0.432637918980507
cg00010445_TC21 0.859746885326994
cg00010903_BC21 0.486178921591465
cg00010926_BC21 0.940317364626035
cg00010977_TC21 0.915160047738774
cg00012521_TO21 0.526922890790931
cg00012879_TC21 0.489799041849299
cg00013189_BC11 0.0154179002285135

Total number of rows: 326732

Table truncated, full table size 10861 Kbytes.




Supplementary file Size Download File type/resource
GSM7008076_206535570058_R04C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008076_206535570058_R04C01_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