GEO series

Augmented Drug Resistance of Osteosarcoma Cells within Decalcified Bone Matrix Scaffold: the role of Glutamine Metabolism

GSE234632 Homo sapiens (human) RNA-seq (gene expression) 6 samples Submitted 2023/12/20 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 6 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: OsteosarcomaThis series is part of our curated briefing on it.
Samples: 6 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Due to the lack of a precise in vitro model that can mimic the nature microenvironment in osteosarcoma, the understanding of its resistance to chemical drugs remains limited. Here, we report a novel three-dimensional model of osteosarcoma constructed by seeding tumor cells (MG-63 and MNNG/HOS Cl #5) within in demineralized bone matrix scaffolds.

Read the full summary ↓

Demineralized bone matrix scaffolds retain the original components of the natural bone matrix (hydroxyapatite and collagen type I), and possess good biocompatibility allowing osteosarcoma cells to proliferate and aggregate into clusters within the pores. Growing within the scaffold conferred elevated resistance to doxorubicin on MG-63 and MNNG/HOS Cl #5 cell lines as compared with two-dimensional cultures. Transcriptomic analysis showed an increased enrichment for drug resistance genes along with enhanced glutamine metabolism in osteosarcoma cells in demineralized bone matrix scaffolds. Inhibition of glutamine metabolism resulted a decrease in drug resistance of osteosarcoma, which could be restored by α-ketoglutarate supplementation. Overall, our study suggests that microenvironmental cues in demineralized bone matrix scaffolds can enhance osteosarcoma drug responses and that targeting glutamine metabolism may be a strategy for treating osteosarcoma drug resistance.

This dataset

Open GSE234632 in finder → Find more human RNA-seq datasets → Osteosarcoma landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE234632_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA982159 and SRA study SRP442137. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

More Osteosarcoma datasets

GSE296989 Gene Expression Modulation by Ultrasound-Responsive Biocatalytic 3D Scaffolds for Controlled Osteosarcoma Cell Elimination and Rat Cranial Bone Regeneration 15 samples same disease briefing · shares osteosarcoma, scaffold
GSE268415 PRKDC Induces Chemoresistance in Osteosarcoma by Recruiting GDE2 to Stabilize GNAS and Activate AKT 12 samples same disease briefing · shares osteosarcoma, resistance
GSE317900 ZDHHC8-mediated β-catenin palmitoylation promotes WNT signaling activation and drives cisplatin resistance in osteosarcoma 8 samples same disease briefing · shares osteosarcoma, resistance
GSE270231 Aberrant activation of wound healing programs within the metastatic niche facilitates lung colonization by osteosarcoma cells 7 samples same disease briefing · shares osteosarcoma, within
GSE21257 Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19) 53 samples same disease briefing · shares osteosarcoma, within
GSE154540 CDK4 overexpression is a predictive biomarker for resistance to conventional chemotherapy in osteosarcoma patients 50 samples same disease briefing · shares osteosarcoma, resistance
GSE259286 In vitro modeling of nutritional and mitochondrial-targeted therapies for osteosarcoma 98 samples same disease briefing · shares osteosarcoma
GSE253548 The whole transcriptome analysis using FFPE and fresh tissue samples identifies the molecular fingerprint of osteosarcoma 90 samples same disease briefing · shares osteosarcoma

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.