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Table 1 Information of the included datasets

From: Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval

CategoryGEO accession numberPlatformSample typeSample sizeExperiment design
GeneTumor vs. normalGSE11414GPL6244Cell linesTumor: 4; normal: 2genome-wide comparison of gene expression and identified genes that are differentialy expressed in osteosarcoma (U2OS, MG63) cell lines relative to normal human osteoblasts (HOB)
GSE12865GPL6244Tumor tissues and normal cell lineTumor: 12; normal: 2genome-wide comparison of gene expression and identified genes that are differentialy expressed in osteosarcoma tumour samples relative to normal human osteoblasts (HOB)
GSE14359GPL96Tumor tissues and normal cell lineTumor: 18; normal: 2mRNA from 5 frozen conventional osteosarcoma and 4 osteosarcoma lung metastases tumor samples and mRNA from fresh primary osteoblast cells (HOB) were extracted and hybridized to HG U133A microarrays
GSE16088GPL96Tumor and normal tissues, as well as tumor cell linesTumor: 17; normal: 6Profiles of human osteosarcoma and three normal tissues, single channel design
GSE19276GPL6848Tumor and normal tissuesTumor: 44; normal: 5Gene expression profiling of primary osteosarcoma biopsies and compared the results to gene expression profiling of non-malignant bone to identify differentially expressed genes unique to OS in the context of the bone micorenvironment
GSE28424GPL13376Tumor cell lines and normal tissuesTumor: 19; normal: 419 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones.
GSE30807GPL570Tumor cell lines and normal bone mesenchymal stem cellsTumor: 2; normal: 1To analysis stem/progenitor cell-associated genes and molecules involved in regulation of self-renewal signaling pathways of cancer stem cells between UT2 cells and its parent cells: U2OS (MSC works as positive control here)
GSE36001GPL6102Tumor cell lines and normal osteoblast and bone cells.Tumor: 19; normal: 6Comparison of gene expression patterns in 19 osteosarcoma cell lines and 6 normal samples (osteoblasts and bones)
GSE42352GPL10295Tumor cell lines, pre-chemotherapy biopsies, osteoblasts, mesenchymal stem cellsTumor: 103; normal: 15Gene set analysis on previously published genome-wide gene expression data of osteosarcoma cell lines (n = 19) and osteosarcoma pre-chemotherapy biopsies (n = 84), and characterizing expression of the insulin-like growth factor receptor signaling pathways in human osteosarcoma as compared with osteoblasts and with the hypothesized progenitor cells of osteosarcoma - mesenchymal stem cells.
GSE56001GPL10558Tumor cells and normal mesenchymal stem cellsTumor: 3; normal: 9Analysis of gene changes in different genes modulation in mesenchymal stem cells and compared to primary human osteosarcoma cells
GSE9508GPL6076Tumor and normal biopsiesTumor: 34; normal: 5Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates).
Metastasis vs. non-metastasisGSE14359GPL96Conventional osteosarcoma and lung metastases tumor samplesMetastasis: 8; non-metastasis: 10mRNA from 5 frozen conventional osteosarcoma and 4 osteosarcoma lung metastases tumor samples and mRNA from fresh primary osteoblast cells (HOB) were extracted and hybridized to HG U133A microarrays
GSE18947GPL570Low and high metastatic potential cell sublinesLow metastasis: 3; high metastasis: 3The assay was performed among three pairs of cublines, the first two pairs of sublines comes from the different passage of sublines established with orthotopic transplantation under the established cell line named Sosp-9607, the other pair was screened by the tail-vein injection method of commercial avaliable cell line-Saos-2.
GSE21257GPL10295Metastatic and non-metastatic tumor biopsiesMetastasis: 34; non-metastasis: 19Pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5 yrs. (n = 34) were compared with pre-chemotherapy biopsies of osteosarcoma patients who did not develop metastases within 5 yrs. (n = 19)
GSE9508GPL6076Metastatic and non-metastatic tumor biopsiesMetastasis: 21; non-metastasis: 13Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates).
Drug-treated vs. untreatedGSE16089GPL570Methotrexate-sensitive and –resistant Saos-2 cellsMethotrexate-sensitive samples: 3; methotrexate-resistant samples: 3Two cell lines are compared, which are Saos-2 osteosarcoma cells sensitive to methotrexate and Saos-2 cells resistant to 10e-6 M methotrexate. Six samples are provided which correspond to triplicates of each cell line.
GSE24401GPL1456Atorvastatin-treated and -untreated Saos-2 cellsAtorvastatin-treated samples: 3; atorvastatin-untreated samples: 3Dye balance-experiment comparing atorvastatin treated Saos-2 cells versus untreated cells at 6, 15 and 24 h using 2 biological replicates
miRNAGSE28423GPL8227Tumor cell lines and normal bonesTumor cell lines: 19; normal bones: 419 osteosarcoma cell lines, 4 normal bones used as controls. No replicates. The group of osteosarcomas are compared to the group of normal bones.
CNVGSE12830GPL4091, GPL9128Tumor tissues20Integrative whole-genome analysis of DNA copy number, promoter methylation and gene expression using 10 osteosarcomas with 2 biological replicates
GSE7077GPL2879Four osteosarcoma-derived cell lines: U-2 OS, HOS, MG-63 and SAOS-24To utilize oligonucleotide array CGH to identify microaberrations in osteosarcomas, likely to contain genes involved in osteosarcoma tumor oncogenesis. A better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of prognostic markers and therapeutic targets.
GSE9654GPL2879 10To utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in osteosarcoma tumors
  1. “-” in the column of “PubMed ID” means that there is no published study so far. GEO Gene Expression Omnibus, CGH Comparative genomic hybridization, FISH Fluorescence in situ hybridization