Table 2.
Overview of –omics data resources from human bone tissue by technology.
| Description (author) | Number of samples | Availability of data | assessment type: global or targeted |
|---|---|---|---|
| Proteomics | |||
| Immunological quantification of targeted proteins from postmenopausal iliac bone biopsies (185, 186) | 56 | Authors/publication | Targeted (SOST, DKK1, sFRP3, WIF1) |
| Western analysis of postmenopausal intertrochanteric bone biopsies (25 osteoporotic with fracture + 29 with OA) (187) | 54 | Authors/publication | Targeted (DKK1, β-catenin) |
| LC-MS analysis of young adult alveolar bone from two healthy females and two males (aged 15−21 years) (188) | 4 | PRIDE Project PXD011524 | Global |
| Stable isotope labeling by amino acids in cell culture (SILAC) analysis of primary cultured human osteoblasts co-cultured with human umbilical vein endothelial cells (HUVECs) (189) | 2 | PRIDE Project PXD011844 | Global |
| Shotgun proteomics (LC-MS) of archeological human bone from 4 adults and 2 infants (190) | 6 | PRIDE Project PXD006256 | Global |
| LC-MS/MS analysis of cranial suture samples stripped of periosteum from 5 infants (ages 3–12 months) (191) | 10 | PRIDE Project PXD003215 | Global |
| LC-MS/MS analysis of alveolar bone and dental cementum from 5 females and 2 males ranging from 20 to 30 years old. (192) | 7 | PRIDE Project PXD000420 | Global |
| Transcriptomics | |||
| RNA-seq of transiliac bone biopsies and subchondral femoral head samples (Prijatelj et al.) publication in progress | 121 | Authors | Global |
| eQTL analysis of transiliac bone biopsies (Prijatelj, Reppe et al.) publication in progress | 76 | Authors | Global |
| RNA-seq of purified osteoblasts from male iliac bone biopsies (127) | 6 | Authors/publication | Global |
| Microchip RNA profiling of postmenopausal transiliac bone biopsies (193) | 84 | EMBL-EBI repository, ID: E-MEXP-1618. | Global |
| PCR based and microchip profiling of postmenopausal iliac or femoral bone biopsy ncRNAs. (194) | 84 + 18 | Authors/publication | Global |
| Microchip RNA profiling of 19 spine and 5 iliac crest bone biopsies from 13 male donors. (195) | 24 | EMBL-EBI repository, ID: E-MEXP-2219 | Global |
| Microchip profiling of postmenopausal intertrochanteric bone biopsies (10 with OA + 10 osteoporotic + 10 autopsies from controls) (196, 197) | 30 | Authors/publication | Global |
| PCR profiling of postmenopausal intertrochanteric bone biopsies (25 osteoporotic with fracture + 29 with OA) (187) | 54 | Authors/publication | Targeted, including mRNAs and miRNAs |
| PCR profiling of postmenopausal/male intertrochanteric femoral bone biopsies (49 with OA + 50 osteoporotic + 14 autopsies from controls) (198–200) | 113 | Authors/publication | Targeted |
| PCR profiling of femoral head bone biopsies from non-osteoporotic women (10 postmenopausal + 7 pre-menopausal) (201, 202) | 16 | Authors/publication | Targeted (>150 genes) |
| PCR profiling of male iliac crest bone biopsies (9 osteoporotic + 9 healthy) (203) | 18 | Authors/publication | Targeted |
| PCR profiling of elderly male femoral head bone biopsies (12 with osteoporosis/fracture + 10 with OA) (204) | 22 | Authors/publication | Targeted |
| PCR profiling after fracture of male and female femoral bone biopsies (45 with fracture/osteoporosis + 15 with fracture/non-osteoporotic) (205) | 60 | Authors/publication | Targeted |
| miRNA profiling of postmenopausal femoral neck bone biopsies (6 with osteoporosis + 10 with OA) and primary cultured osteoblasts from knee (n=4) (206) | 16 | Authors/publication | Global |
| miRNA profiling of postmenopausal femoral head biopsies (27 with fracture + 27 with OA) (207) | 54 | Authors/publication | Global |
| mRNA and miRNA PCR profiling of postmenopausal or male femoral bone biopsies after fracture (20 osteoporotic + 20 non-osteoporotic) (208) | 40 | Authors/publication | Targeted |
| PCR profiling of postmenopausal and male femoral bone (6 osteoporotic + 20 with OA) (209) | 12 | Authors/publication | Targeted (172 genes) |
| RNA-seq of centrifuged postmenopausal iliac crest bone biopsies from denosumab treated or untreated donors (210) | 30 | GEO Accession: GSM4209348 | Global |
| RNA-seq of explant osteoblast cultures from human patients with non-syndromic craniosynostosis (n=23) and controls (n=8) (211) | 31 | GEO Accession: GSM1333404 | Global |
| Microchip profiling of transiliac crest bone biopsies from 9 patients with endogenous Cushings syndrome before and after treatment (212) | 18 | GEO Accession: GSE30159 | Global |
| Microchip profiling of transiliac crest bone biospies from 7 patients with primary hyperparathyroidism before and one year after parathyroidectomy (213, 214) | 14 | EMBL-EBI: E-MEXP-847 | Global |
| Microchip profiling of transiliac bone biopsies from 2 male controls and 2 male patients with clinically characterized Fibrogenesis imperfecta ossium (215) | 4 | GEO Accession: GSE43861 | Global |
| RNA-seq of centrifuged postmenopausal iliac crest bone biopsies from young women (n=19), postmenopausal women treated with estrogen (n=20) and postmenopausal controls (n=19). (216) | 58 | GEO Accession: GSE72815 | Global |
| Microchip profiling of osteoclasts treated with bisphosphonates (n=6) and controls (n=3) (217) | 9 | GEO Accession: GSM1537946 | Global |
| Microchip profiling of primary osteoclast precursors differentiated with CSF-1 and RANKL or CSF-1 alone (115) | 4 | GEO Accession: GSE107297 | Global |
| Microchip profiling of OA (n = 20) and non-OA (n = 5) knee lateral tibial and medial tibial plateaus subchondral bone biopsies. (218) | 50 | EMBL-EBI: GSE51588 | Global |
| DNA methylation | |||
| Microchip DNA methylation profiling of postmenopausal transiliac bone biopsies (219, 220) | 84 | Authors/publication | Global |
| Microchip DNA methylation profiling of postmenopausal femoral bone biopsies (221) | 30 | Authors/publication | Global |
| PCR/pyrosequencing of femoral head bone DNA from postmenopausal women/elderly men subjected to hip replacement due to fracture or OA and RNA expression analysis of RANKL, OPG and BGLAP (222) | 21 | Authors/publication | Targeted |
| Sequencing of bisulfite-converted femoral bone DNA from 32 males or females with fracture, of whom 16 were non-osteoporotic and RNA expression analysis of RANKL, OPG, SOST (223, 224) | 32 | Authors/publication | Targeted |
| Sequencing of bisulfite-converted femoral bone DNA from 20 postmenopausal women with fracture, of which 8 were non-osteoporotic, and RNA expression analysis of SP7, RUNX2, SOST, ERα (225) | 20 | Authors/publication | Targeted |
| Microchip DNA methylation profiling of mesenchymal stem cells from postmenopausal femoral head bone biopsies (22 with fracture and 17 with OA) and RNA-seq of MSC samples from 10 women with fracture and 10 women with OA (136) | 39 | Authors/publication | Global |
| RRBS of primary cultured osteoblasts (226) | 2 | GSM683881, GSM683928 | Global |
| Microchip DNA methylation profiling, changes during monocytes to osteoclast differentiation (227) | 6 | EMBL-EBI: GSE46648 | Global |
| Microchip DNA methylation profiling of femoral head trabecular bone biopsies from females (n=46) and males (n=2). (228) | 48 | EMBL-EBI: GSE64490 | Global |
| Pyrosequencing of DNA from human osteoclasts generated from women ages 40 to 66 years. Differentiation, fusion, bone resorption, and in vivo characteristics were evaluated in the context of DNA methylation of DCSTAMP and CTSK (156, 157) | 49 | Authors/publication | Targeted |
| Chromatin structure | |||
| Hi-C and RNA-sec of primary cultured human osteocytes (Hsu, Kiel et al.; publication in progress) | 1 | Authors | Global |
| Dnase1-seq, ChIP-seq (H3K4me3), 5C and RNA-seq of primary cultured osteoblasts. (229) | 1 | GEO Accessions: DNase1-seq: GSE29692, GSE32970; ChIP-seq: GSE35583; RNA-seq: GSE19090, GSE15805, GSE17778; 5C: wgEncodeEH002102 | Global |
| ATAC-seq, RNA-seq and 3C analysis of osteoblasts and adipocytes derived from human bone-marrow MSC (230) | 4 | European Bioinformatics Institute (EMBL-EBI) Capture C: E-MTAB-6862; ATAC-Seq: E-MTAB-6834; RNA-Seq: E-MTAB-6835 | Global |
| ChIP-seq and RNA-seq experiments in MSC and immortalized osteoblastic cells (hFOB 1.19) before and after differentiation. ChIP-seq was done for H2A.Z, H2Bub1, H3.3, RNAPII and CHD1 in differentiated FOB with control or CHD1 siRNA treatment (231) | 35 | GEO Accession: GSE89179 | Global |
| DNase1-seq and microchip RNA profiling of immortalized osteoblastic cells (hFOB 1.19) before and after differentiation (232) | 10 | GEO Accession: GSE75232 | Global |
| Chip-seq of primary cultured osteoblasts in which DNA was precipitated with 11 different histone antibodies (233) | 11 | ENCSR786NTC | Global |
| DNase1-seq of bones from female and male embryos (98 and 81 days, respectively) (234, 235) | 5 | ENCSR805XIF, ENCSR976XOY, ENCSR431UEM, ENCSR274SDO, ENCSR449HOQ | Global |
The data was generated based on searches in PubMed and the following portals: ProteomeXchange Data http://proteomecentral.proteomexchange.org/cgi/GetDataset; Sequence Read Archive (SRA) https://www.ncbi.nlm.nih.gov/sra; Gene Expression Omnibus (GEO) https://www.ncbi.nlm.nih.gov/geo/; OmicsDI https://www.omicsdi.org/; SkeletalVis http://phenome.manchester.ac.uk/; Array Express https://www.ebi.ac.uk/arrayexpress/; ENCODE https://www.encodeproject.org/search/?searchTerm=bone. Search finished by May 6th 2020.