Skatole attenuates osteoarthritis by protecting chondrocytes and mediating macrophage repolarization through regulating the NFκB/MAPK signaling pathway and metabolic reprogramming II
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 3 × macrophages D vs 3 × macrophages D+L vs 3 × macrophages L+SGroups 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.
- Paper
- Skatole Alleviates Osteoarthritis by Reprogramming Macrophage Polarization and Protecting ChondrocytesResearch (Washington, D.C.) · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE283748_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1195129 and SRA study SRP549860. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 10 sample titles; they account for 9 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.
- GSM8671585 macrophages Blank
- GSM8671586 macrophages D_1 macrophages D
- GSM8671587 macrophages D_2 macrophages D
- GSM8671588 macrophages D_3 macrophages D
- GSM8671589 macrophages D+L_1 macrophages D+L
- GSM8671590 macrophages D+L_2 macrophages D+L
- GSM8671591 macrophages D+L_3 macrophages D+L
- GSM8671592 macrophages L+S_1 macrophages L+S
- GSM8671593 macrophages L+S_2 macrophages L+S
- GSM8671594 macrophages L+S_3 macrophages L+S
- GSE278577 β2 ADRENERGIC SIGNALING STIMULATES EARLY IL-1β SECRETION IN MACROPHAGES BY INDUCING MAPK-DEPENDENT Il1b TRANSCRIPTION [RNA-Seq] 30 samples shares mapk, macrophage
- GSE248058 Stroma reprogramming by FAK synergizes with MAPK inhibition and renders PDAC responsive to cytotoxic- and immuno-therapies II 18 samples shares mapk, reprogramming
- GSE335147 Mitochondrial profiling across macrophage states reveals inhibition of IL-4/IL-13 reprogramming by the integrated stress response 24 samples shares reprogramming, macrophage
- GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares reprogramming, macrophage
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares reprogramming, macrophage
- GSE261139 Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential 16 samples shares reprogramming, macrophage
- GSE307773 Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq] 175 samples shares mapk
- GSE234245 Multiomic Profile Integration Reveals Early Signatures of Amyotrophic Lateral Sclerosis and Suggests the MAPK Pathway as a Therapeutic Target [RNA-Seq] 79 samples shares mapk
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.