|
| Status |
Public on Aug 07, 2023 |
| Title |
P30.Dataset, 206535570093_R01C01 |
| Sample type |
genomic |
| |
|
| Source name |
206535570093_R01C01
|
| Organism |
Mus musculus |
| Characteristics |
age: 0.534246575
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) |
|
