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Sample GSM7007996 Query DataSets for GSM7007996
Status Public on Aug 07, 2023
Title P30.Dataset, 206535570093_R01C02
Sample type genomic
 
Source name 206535570093_R01C02
Organism Mus musculus
Characteristics age: 0.520547945
confidenceinageestimate: 100
tissue: Kidney
female: 0
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 0.46863205033507
cg00001209_TC21 0.934536574942384
cg00001364_TC21 0.946820811936378
cg00001582_TC21 0.0422173726626499
cg00002920_TC21 0.278476149119361
cg00003994_TC21 0.032371932171096
cg00004555_BC21 0.0393186215203112
cg00005112_TC21 0.827631495806452
cg00005271_TC21 0.970689631124654
cg00006213_TC21 0.8297420346955
cg00008998_TC21 0.496202990723623
cg00009248_TC21 0.949511481755332
cg00009319_BC21 0.407007534457828
cg00010445_TC21 0.75197466897601
cg00010903_BC21 0.482324207459631
cg00010926_BC21 0.950272002773925
cg00010977_TC21 0.905389925691619
cg00012521_TO21 0.517601933476329
cg00012879_TC21 0.516722208359806
cg00013189_BC11 0.0182448925975696

Total number of rows: 326732

Table truncated, full table size 10860 Kbytes.




Supplementary file Size Download File type/resource
GSM7007996_206535570093_R01C02_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7007996_206535570093_R01C02_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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