NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7008169 Query DataSets for GSM7008169
Status Public on Aug 07, 2023
Title P31.Dataset, 206535570091_R01C01
Sample type genomic
 
Source name 206535570091_R01C01
Organism Mus musculus
Characteristics age: 0.498630137
confidenceinageestimate: 100
tissue: Blood
female: 0
tissuedetailed: Whole blood
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 0.439929095401977
cg00001209_TC21 0.924173691157256
cg00001364_TC21 0.904717584727272
cg00001582_TC21 0.0596319461020492
cg00002920_TC21 0.142583398156273
cg00003994_TC21 0.0351644114806006
cg00004555_BC21 0.113699723198444
cg00005112_TC21 0.918736673717146
cg00005271_TC21 0.96166805984027
cg00006213_TC21 0.918646853038164
cg00008998_TC21 0.4911072383484
cg00009248_TC21 0.936732174831229
cg00009319_BC21 0.366218302081972
cg00010445_TC21 0.823931731314501
cg00010903_BC21 0.493542942564019
cg00010926_BC21 0.93091145255294
cg00010977_TC21 0.90575101017529
cg00012521_TO21 0.509801693276085
cg00012879_TC21 0.505006504702912
cg00013189_BC11 0.0218635250045489

Total number of rows: 326732

Table truncated, full table size 10862 Kbytes.




Supplementary file Size Download File type/resource
GSM7008169_206535570091_R01C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008169_206535570091_R01C01_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
External link. Please review our privacy policy.