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Sample GSM7008052 Query DataSets for GSM7008052
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570112_R04C01
Sample type genomic
 
Source name 206535570112_R04C01
Organism Mus musculus
Characteristics age: 0.536986301
confidenceinageestimate: 100
tissue: Cortex
female: 1
tissuedetailed: Cortex
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 0.515804871818689
cg00001209_TC21 0.48394629626958
cg00001364_TC21 0.912169567789259
cg00001582_TC21 0.0474069883913127
cg00002920_TC21 0.520748925911486
cg00003994_TC21 0.0383754414770931
cg00004555_BC21 0.0966917357021035
cg00005112_TC21 0.458965697804682
cg00005271_TC21 0.771864395132235
cg00006213_TC21 0.730581360372552
cg00008998_TC21 0.484331102463927
cg00009248_TC21 0.830820397293862
cg00009319_BC21 0.419619419550076
cg00010445_TC21 0.548288967717295
cg00010903_BC21 0.513805747687265
cg00010926_BC21 0.891377879394388
cg00010977_TC21 0.6868017058235
cg00012521_TO21 0.451454242266436
cg00012879_TC21 0.517298123425843
cg00013189_BC11 0.0132071116035618

Total number of rows: 326732

Table truncated, full table size 10858 Kbytes.




Supplementary file Size Download File type/resource
GSM7008052_206535570112_R04C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008052_206535570112_R04C01_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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