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Sample GSM2759620 Query DataSets for GSM2759620
Status Public on Mar 14, 2020
Title genomic DNA from healthy adult distal femur trabecular bonePanu48_B (baboon_intraspecific)
Sample type genomic
 
Source name healthy adult distal femur trabecular bone from baboon
Organism Papio sp.
Characteristics Sex: female
age (years): 11.13
steady state weight (kg): 16.49
tissue: bone
age cohort: adult
disease state: healthy
femur length (mm): 201
bicondylar femur length (mm): 198
maximum femur length (mm): 197
superior shaft width (mm): 14.31
superior shaft depth (mm): 15.17
middle shaft width (mm): 13.65
middle shaft depth (mm): 14.12
inferior shaft width (mm): 23.98
inferior shaft depth (mm): 15.59
head height (mm): 22.35
head length (mm): 22.19
head width (mm): 16.51
anatomical neck length (mm): 14.07
anatomical neck height (mm): 14.59
anatomical neck depth (mm): 12.26
biomechanical neck length (mm): 38.5
proximal width (mm): 40.82
lesser trochanter to head (mm): 38.63
lesser trochanter to neck (mm): 31.18
lesser to greater trochanter (mm): 45.31
medial condyle height (mm): 19.6
medial condyle depth (mm): 28.67
medial condyle width (mm): 12.47
lateral condyle height (mm): 19.53
lateral condyle depth (mm): 28.74
lateral condyle width (mm): 12.93
intercondylar notch width (mm): 9.17
intercondylar notch depth (mm): 13.39
bicondylar width (mm): 33.37
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted from pulverized trabecular bone 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 Mar 14, 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 (2)
GSE103279 Assessment of DNA methylation patterns related to femur bone morphology in baboon bone using the 850K array
GSE103332 Intra- and Inter-Specific Investigations of Skeletal DNA Methylation Patterns and Femur Morphology in Nonhuman Primates

Data table header descriptions
ID_REF
VALUE Average Beta

Data table
ID_REF VALUE
cg00000029 0.87535736
cg00000165 0.060195325
cg00000221 0.752513607
cg00000236 0.84105252
cg00000714 0.466361234
cg00000924 0.577789203
cg00001136 0.661802917
cg00001364 0.889090984
cg00001446 0.896141177
cg00001582 0.026259314
cg00001747 0.048182523
cg00001793 0.827710866
cg00001810 0.804758658
cg00002028 0.063297914
cg00002033 0.012197913
cg00002080 0.880693695
cg00002186 0.86558037
cg00002236 0.028042963
cg00002350 0.87180001
cg00002366 0.843126905

Total number of rows: 189858

Table truncated, full table size 4243 Kbytes.




Supplementary file Size Download File type/resource
GSM2759620_200669350047_R07C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM2759620_200669350047_R07C01_Red.idat.gz 7.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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