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3D-printed nHA/PA66 porous scaffold: Regulating immune balance and vascularization synergistically promotes bone regeneration

GSE302075 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/12/31 Platform GPL21103Platform GPL20301
At a glance

RNA-seq (gene expression) · mouse · 24 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
Mus musculus (mouse)
Samples
24 samples: 8 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)
3D-printed porous scaffolds have emerged as a potential solution for treating critical-sized bone defects, yet localized inflammatory imbalance leads to suboptimal therapeutic outcomes. This study utilized nHA/PA66 composite material as the foundation, employing APF additive manufacturing technology to fabricate a three-dimensional porous scaffold (HP) suitable for local bone filling, and functionalized the porous scaffold through modification with polydopamine and magnesium ions (Mg2+) (HPDM).
Read the full summary ↓
First, the physicochemical properties and biosafety of the HPDM scaffold were verified, followed by a comparative analysis of its effects on macrophage phenotype transformation, vascular endothelial cell differentiation, and pre-osteoblast differentiation differences. The HPDM scaffold achieves coordinated balance in the transformation between M1 and M2 macrophages through sustained release of polydopamine and Mg2+. Mg2+ plays a crucial role in inflammatory regulation by downregulating the NF-κB signaling pathway. Furthermore, several experiments demonstrated that the HPDM scaffold regulates orderly inflammatory responses to promote intercellular interactions, stimulating angiogenesis and osteogenic regeneration. In New Zealand rabbits' femoral condyle bone defect model, the HPDM porous scaffold achieved significant vascularized bone regeneration. This study confirms that the functionalized HPDM porous scaffold prepared using nHA/PA66 as the base material has significant potential in regulating immune responses and enhancing vascularized bone regeneration.
This dataset
Open GSE302075 in finder → Find more RNA-seq datasets →
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 GSE302075_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 PRJNA1288468 and SRA study SRP599237. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
MC3T3-E1 CELLS, HP group, 7days ×3 MC3T3-E1 CELLS, HPD group, 7days ×3 MC3T3-E1 CELLS, HPDM group, 7days ×3 MC3T3-E1 CELLS, HPDM@Hu/Ra group, 7days ×3 RAW 264.7 CELLS, HP group, 3days ×3 RAW 264.7 CELLS, HPDM group, 3days ×3 HUVEC CELLS, HP group, 3days ×3 HUVEC CELLS, HPDM group, 3days ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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