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Sample GSM7008021 Query DataSets for GSM7008021
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570108_R02C02
Sample type genomic
 
Source name 206535570108_R02C02
Organism Mus musculus
Characteristics age: 0.536986301
confidenceinageestimate: 100
tissue: Spleen
female: 1
tissuedetailed: Spleen
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 0.482996327108643
cg00001209_TC21 0.922590603914277
cg00001364_TC21 0.95252393350965
cg00001582_TC21 0.0498275896088636
cg00002920_TC21 0.192910823931394
cg00003994_TC21 0.0642528994403287
cg00004555_BC21 0.13108597807751
cg00005112_TC21 0.924194350414925
cg00005271_TC21 0.972568765585157
cg00006213_TC21 0.889930606168697
cg00008998_TC21 0.496405093394857
cg00009248_TC21 0.885901294156967
cg00009319_BC21 0.352282809748402
cg00010445_TC21 0.879052250082
cg00010903_BC21 0.504696673691479
cg00010926_BC21 0.829309063298796
cg00010977_TC21 0.950965365877408
cg00012521_TO21 0.501486340398561
cg00012879_TC21 0.455426542895127
cg00013189_BC11 0.016737211509225

Total number of rows: 326732

Table truncated, full table size 10852 Kbytes.




Supplementary file Size Download File type/resource
GSM7008021_206535570108_R02C02_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008021_206535570108_R02C02_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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