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Sample GSM2759775 Query DataSets for GSM2759775
Status Public on Dec 28, 2020
Title genomic DNA from healthy adult distal femur articular cartilage Panu34_C (baboon_oa)
Sample type genomic
 
Source name healthy adult distal femur articular cartilage from baboon
Organism Papio sp.
Characteristics Sex: female
age (years): 16.51
steady state weight (kg): 22.34
tissue: cartilage
age cohort: adult
disease state: healthy
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted from pulverized trabecular bone or homogenized cartilage using a phenol-cholorform protocol
Label Cy5 and Cy3
Label protocol 400ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)
 
Hybridization protocol Infinium MethylationEPIC array
Scan protocol standard illumina scanner
Description medial condyle healthy adult distal femur articular cartilage from baboon
Data processing Raw fluorescent data were normalized using the Noob background correction method with dye-bias normalization followed with a between-array normalization method (functional normalization) as implemented in the R package minfi. After normalization, methylation values (beta values) for each site were calculated as the ratio of methylated probe signal intensity to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than 10% of samples were removed. Cross-reactive probes, probes containing SNPs at the CpG site, probes detecting SNP information, probes detecting methylation at non-CpG sites, and probes targeting sites within the sex chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to each nonhuman primate genome were also removed. Filtering for these files was based on Hernando-Herraez et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate nonhuman primate genome, and only those probes that successfully mapped to the genome, had only 1 unique hit, and targeted CpG sites were retained. Additionally, probes were kept for subsequent analyses only if they had 0 mismatches in 5bp closest to and including the CpG site, and had 0-2 mismatches in 45bp not including the CpG site.
- Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and great ape evolution. PLOS Genet 2013;9:e1003763.
Nonhuman Primate Genome: Papio anubis
 
Submission date Aug 30, 2017
Last update date Dec 28, 2020
Contact name Genevieve Housman
E-mail(s) ghousman@uchicago.edu
Organization name University of Chicago
Department Genetic Medicine
Street address 920 East 58th Street, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL21145
Series (1)
GSE103286 Assessment of DNA methylation patterns related to osteoarthritis in baboon bone and cartilage using the 850K array

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.885560983
cg00000165 0.051398147
cg00000221 0.769865079
cg00000236 0.849389083
cg00000714 0.05140736
cg00000924 0.628261639
cg00001136 0.535010975
cg00001364 0.893239807
cg00001446 0.776565055
cg00001582 0.024944093
cg00001747 0.013905551
cg00001793 0.906913565
cg00001810 0.825292882
cg00002028 0.079327333
cg00002033 0.022407491
cg00002080 0.912898035
cg00002186 0.7814318
cg00002236 0.027669117
cg00002350 0.697499895
cg00002366 0.390874337

Total number of rows: 191954

Table truncated, full table size 4290 Kbytes.




Supplementary file Size Download File type/resource
GSM2759775_200669350048_R03C01_Grn.idat.gz 6.8 Mb (ftp)(http) IDAT
GSM2759775_200669350048_R03C01_Red.idat.gz 7.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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