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Sample GSM2759730 Query DataSets for GSM2759730
Status Public on Dec 28, 2020
Title genomic DNA from healthy adult distal femur trabecular bone Panu19_B (baboon_oa)
Sample type genomic
 
Source name healthy adult distal femur trabecular bone from baboon
Organism Papio sp.
Characteristics Sex: female
age (years): 19.59
steady state weight (kg): 18.84
tissue: bone
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 trabecular bone 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 0.857037923
cg00000165 0.09357741
cg00000221 0.815521064
cg00000236 0.795386169
cg00000714 0.252891445
cg00000924 0.698254442
cg00001136 0.797948205
cg00001364 0.908069068
cg00001446 0.776757699
cg00001582 0.031943352
cg00001747 0.018065734
cg00001793 0.945568284
cg00001810 0.823082994
cg00002028 0.161478218
cg00002033 0.095331235
cg00002080 0.865733897
cg00002186 0.858681181
cg00002236 0.034799183
cg00002350 0.66433668
cg00002366 0.497689131

Total number of rows: 191954

Table truncated, full table size 4290 Kbytes.




Supplementary file Size Download File type/resource
GSM2759730_200670680022_R02C01_Grn.idat.gz 6.8 Mb (ftp)(http) IDAT
GSM2759730_200670680022_R02C01_Red.idat.gz 7.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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