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Sample GSM7007994 Query DataSets for GSM7007994
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570093_R05C01
Sample type genomic
 
Source name 206535570093_R05C01
Organism Mus musculus
Characteristics age: 0.490410959
confidenceinageestimate: 100
tissue: Kidney
female: 1
tissuedetailed: Kidney
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 0.490022856798667
cg00001209_TC21 0.913531397444015
cg00001364_TC21 0.946300434402701
cg00001582_TC21 0.0515266844066253
cg00002920_TC21 0.347559766078709
cg00003994_TC21 0.0258220597556078
cg00004555_BC21 0.0323180912205273
cg00005112_TC21 0.766517542376364
cg00005271_TC21 0.96199370296801
cg00006213_TC21 0.822158012283953
cg00008998_TC21 0.525966556048382
cg00009248_TC21 0.947509258757352
cg00009319_BC21 0.299617425730226
cg00010445_TC21 0.729081883908995
cg00010903_BC21 0.486687821166732
cg00010926_BC21 0.895464819121995
cg00010977_TC21 0.894160435597822
cg00012521_TO21 0.537174005675505
cg00012879_TC21 0.482307918267024
cg00013189_BC11 0.0185463092885692

Total number of rows: 326732

Table truncated, full table size 10857 Kbytes.




Supplementary file Size Download File type/resource
GSM7007994_206535570093_R05C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7007994_206535570093_R05C01_Red.idat.gz 2.9 Mb (ftp)(http) IDAT
Processed data included within Sample table

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