|
| Status |
Public on Aug 05, 2023 |
| Title |
genomic DNA from Groundhog Spleen 205863120012_R01C02 |
| Sample type |
genomic |
| |
|
| Source name |
Spleen
|
| Organism |
Marmota monax |
| Characteristics |
age: NA
confidenceinageestimate: 0
female: 0
speciescommonname: Groundhog
maximumlifespanyears: 14
average_adultweight: 4000
ageatsexualmaturityyears: 1.5013698630137
networktrainingset: no
panmammalianclocktrainingset: no
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
none provided
|
| Label |
Cy5
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
genomic DNA from Groundhog Spleen
|
| 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.
normalized (Sesame) Beta values
|
| |
|
| Submission date |
Jan 25, 2023 |
| Last update date |
Aug 05, 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 |
GPL28271 |
| Series (1) |
|
