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Sample GSM7008086 Query DataSets for GSM7008086
Status Public on Aug 07, 2023
Title P31.Dataset, 206535570006_R02C01
Sample type genomic
 
Source name 206535570006_R02C01
Organism Mus musculus
Characteristics age: 0.512328767
confidenceinageestimate: 100
tissue: Kidney
female: 0
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 0.477118357969135
cg00001209_TC21 0.899787715604587
cg00001364_TC21 0.924121501194471
cg00001582_TC21 0.065511056197353
cg00002920_TC21 0.396764335215911
cg00003994_TC21 0.0300539840796151
cg00004555_BC21 0.0422381984135369
cg00005112_TC21 0.800518088443914
cg00005271_TC21 0.95513374900783
cg00006213_TC21 0.79485315120565
cg00008998_TC21 0.453583328136801
cg00009248_TC21 0.945726026789775
cg00009319_BC21 0.310197367237182
cg00010445_TC21 0.767608178212449
cg00010903_BC21 0.534798928096634
cg00010926_BC21 0.952796239590412
cg00010977_TC21 0.875436957173617
cg00012521_TO21 0.517165326064634
cg00012879_TC21 0.5199745273496
cg00013189_BC11 0.0239842133576434

Total number of rows: 326732

Table truncated, full table size 10862 Kbytes.




Supplementary file Size Download File type/resource
GSM7008086_206535570006_R02C01_Grn.idat.gz 2.8 Mb (ftp)(http) IDAT
GSM7008086_206535570006_R02C01_Red.idat.gz 2.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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