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Sample GSM7008031 Query DataSets for GSM7008031
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570110_R06C01
Sample type genomic
 
Source name 206535570110_R06C01
Organism Mus musculus
Characteristics age: 0.520547945
confidenceinageestimate: 100
tissue: Liver
female: 0
tissuedetailed: Liver
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 0.468347304034159
cg00001209_TC21 0.893615254620831
cg00001364_TC21 0.946914430457768
cg00001582_TC21 0.0514054604043756
cg00002920_TC21 0.606655587024838
cg00003994_TC21 0.036550616066771
cg00004555_BC21 0.0536076724738337
cg00005112_TC21 0.886996063037787
cg00005271_TC21 0.960100479419973
cg00006213_TC21 0.887639675436255
cg00008998_TC21 0.50031212769532
cg00009248_TC21 0.919951747734788
cg00009319_BC21 0.429091110776934
cg00010445_TC21 0.705761483272029
cg00010903_BC21 0.491753143151277
cg00010926_BC21 0.91937185807432
cg00010977_TC21 0.891470726465534
cg00012521_TO21 0.478839305300399
cg00012879_TC21 0.581270024650157
cg00013189_BC11 0.016990770487953

Total number of rows: 326732

Table truncated, full table size 10861 Kbytes.




Supplementary file Size Download File type/resource
GSM7008031_206535570110_R06C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008031_206535570110_R06C01_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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