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Sample GSM7008087 Query DataSets for GSM7008087
Status Public on Aug 07, 2023
Title P31.Dataset, 206535570006_R03C01
Sample type genomic
 
Source name 206535570006_R03C01
Organism Mus musculus
Characteristics age: 0.512328767
confidenceinageestimate: 100
tissue: Kidney
female: 1
tissuedetailed: Kidney
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 0.474829795231766
cg00001209_TC21 0.898295390559187
cg00001364_TC21 0.938037983939657
cg00001582_TC21 0.0522627646535817
cg00002920_TC21 0.346962216972427
cg00003994_TC21 0.0300164209632589
cg00004555_BC21 0.0423564179546215
cg00005112_TC21 0.792422742454114
cg00005271_TC21 0.965377546912504
cg00006213_TC21 0.783901025404287
cg00008998_TC21 0.498468082385272
cg00009248_TC21 0.923576157473023
cg00009319_BC21 0.37677564384561
cg00010445_TC21 0.792348273361493
cg00010903_BC21 0.489331526539104
cg00010926_BC21 0.927399582638761
cg00010977_TC21 0.89378231386811
cg00012521_TO21 0.551805961766718
cg00012879_TC21 0.509013819795209
cg00013189_BC11 0.0240252964936165

Total number of rows: 326732

Table truncated, full table size 10859 Kbytes.




Supplementary file Size Download File type/resource
GSM7008087_206535570006_R03C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008087_206535570006_R03C01_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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