A gene expression profile GSE28424 including 19 human OS cell lines (OS group) and 4 human normal long bone tissue samples (control group) was obtained from GEO database (platform: GPL570: Illumina HumanWG-6 v2.0 expression beadchip). As described in the study of Namløs et al. [13 (link)], the 19 human OS cell lines, HAL, HOS, 143B, IOR/MOS, IOR/OS9, IOR/OS10, IOR/OS14, IOR/OS15, IOR/OS18, SARG, KPD, MG-63, MHM, MNNG/HOS, OHS, OSA, Saos-2, U-2 OS, and ZK-58 were derived from ATCC or different partner laboratories within EuroBoNeT. Cell line authentication was performed by STR DNA profiling using Powerplex 16. The four normal long bone tissue samples were obtained from amputations of cancer patients at the Norwegian Radium Hospital. The processed gene expression matrix file was obtained using Affy package in R software [14 (link)]. Probes with different gene symbols were excluded from this study, and the average value of genes matched to multiple probes was taken as the expression value of the probe.
Humanwg 6 v2.0 expression beadchip
Manufactured by Illumina
The HumanWG-6 v2.0 expression beadchip is a microarray platform designed for the comprehensive analysis of human gene expression. It features probes targeting over 48,000 transcript variants, representing more than 25,000 well-annotated human genes. The beadchip is compatible with Illumina's BeadArray technology, enabling high-throughput, cost-effective, and reproducible gene expression profiling.
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Lab products found in correlation
3 protocols using humanwg 6 v2.0 expression beadchip
1
Comparative Analysis of Osteosarcoma Transcriptomes
2
Gastric Adenocarcinoma Gene Expression Analysis
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A flow diagram of the study is shown in Figure 1 . We systematically searched the GEO database to identify the gastric cancer‐related datasets that were clearly diagnosed as adenocarcinoma and provided the stage and grade of each patient for further analysis. The gene chip raw data of GSE28541 provided by Sangbae et al. 10 were obtained from the GEO database. GSE28541 , based on the GPL13376 platform (Illumina HumanWG‐6 v2.0 expression beadchip), contained 40 tumor samples with a pathologically confirmed diagnosis of STAD. In R, the robust multiple array averaging (RMA) algorithm in the affy package was implemented to preprocess the gene expression profile data. After correcting the background, quantile normalization, and probe summarization, the most variable 10,000 of 25,036 genes were preserved for WGCNA.
3
Gene Expression Profiling of Osteosarcoma
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The Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/gds ) database is a gene expression database created and maintained by the National Center for Biotechnology Information (NCBI). It was founded in 2000 and contains high-throughput gene expression data submitted by research institutions around the world. We downloaded gene expression profile data (GSE42352 and GSE42572) from GEO. Dataset GSE42352 included 25 samples from healthy donors and 25 samples from patients with OS. Gene expression profiling analysis of these samples was performed on Illumina human-6 v2.0 expression beadchip (using nuIDs as identifier) (GPL10295). Dataset GSE42572 was processed by Illumina HumanWG-6 v2.0 expression beadchip (GPL13376). Mesenchymal stromal cells were harvested from the iliac crest of 5 healthy donors and 7 OS patients at diagnosis and cultured until passages 2–5, after which cells were harvested and total RNA was isolated.
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