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Gene Expression Modulation by Ultrasound-Responsive Biocatalytic 3D Scaffolds for Controlled Osteosarcoma Cell Elimination and Rat Cranial Bone Regeneration

GSE296989 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/05/18 Platform GPL24676Platform GPL25947
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
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)
Sonodynamic therapy (SDT) offers high efficiency and controllable precision in tumor eradication, while smart enzyme-mimetic materials enable pH-dependent switching between ROS generation and scavenging. Herein, we present HS-ICTO, a 3D-printed scaffold with ultrasound-triggered activation and microenvironment-responsive enzyme-mimetic properties, designed for spatiotemporally controlled therapeutic applications.
Read the full summary ↓
The HS-ICTO scaffold synergistically enhances tumor elimination via TME-responsive ROS generation coupled with SDT effects, while switching to ROS scavenging in physiological conditions to protect stem cells. We conducted RNA sequencing on human osteosarcoma 143B cells treated with conventional scaffold (HS), HS-ICTO, and HS-ICTO + ultrasound (US), and performed comparative transcriptomic analysis of tissue cells in rat calvarial defect repair models implanted with HS versus HS-ICTO scaffolds.
This dataset
Open GSE296989 in finder → Find more 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 GSE296989_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 PRJNA1262323 and SRA study SRP584840. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly in triplicate
143b_HS ×3 143b_HS-ICTO ×3 143b_HS-ICTO+US ×3 rat_HS ×3 rat_HS-ICTO ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
More Osteosarcoma datasets

Search all RNA-seq datasets in GEO →

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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.