Macrophage depletion alleviates pain-related behaviors in osteoarthritic mice
RNA-seq (gene expression) · mouse · 19 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
- 19 samples: 5 × DRG, DMM AP20187 treated, sample vs 5 × DRG, DMM vehicle treated, sample vs 5 × DRG, naive vehicle treated, sample vs 4 × DRG, naive AP20187 treated, sampleGroups 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
- Acute systemic macrophage depletion in osteoarthritic mice alleviates pain-related behaviors and does not affect joint damagebioRxiv : the preprint server for biology · 2024
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 GSE246252_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: 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 PRJNA1032140 and SRA study SRP468459. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 4 replicated groups read from 19 sample titles; they account for 19 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.
- GSM7865637 DRG, DMM AP20187 treated, sample 58 DRG, DMM AP20187 treate…
- GSM7865638 DRG, DMM AP20187 treated, sample 59 DRG, DMM AP20187 treate…
- GSM7865639 DRG, DMM AP20187 treated, sample 60 DRG, DMM AP20187 treate…
- GSM7865640 DRG, DMM AP20187 treated, sample 61 DRG, DMM AP20187 treate…
- GSM7865641 DRG, DMM AP20187 treated, sample 62 DRG, DMM AP20187 treate…
- GSM7865642 DRG, DMM vehicle treated, sample 32 DRG, DMM vehicle treate…
- GSM7865643 DRG, DMM vehicle treated, sample 33 DRG, DMM vehicle treate…
- GSM7865644 DRG, DMM vehicle treated, sample 34 DRG, DMM vehicle treate…
- GSM7865645 DRG, DMM vehicle treated, sample 63 DRG, DMM vehicle treate…
- GSM7865646 DRG, DMM vehicle treated, sample 64 DRG, DMM vehicle treate…
- GSM7865647 DRG, naive AP20187 treated, sample 1 DRG, naive AP20187 trea…
- GSM7865648 DRG, naive AP20187 treated, sample 3 DRG, naive AP20187 trea…
- GSM7865649 DRG, naive AP20187 treated, sample 4 DRG, naive AP20187 trea…
- GSM7865650 DRG, naive AP20187 treated, sample 5 DRG, naive AP20187 trea…
- GSM7865651 DRG, naive vehicle treated, sample 1 DRG, naive vehicle trea…
- GSM7865652 DRG, naive vehicle treated, sample 2 DRG, naive vehicle trea…
- GSM7865653 DRG, naive vehicle treated, sample 3 DRG, naive vehicle trea…
- GSM7865654 DRG, naive vehicle treated, sample 4 DRG, naive vehicle trea…
- GSM7865655 DRG, naive vehicle treated, sample 5 DRG, naive vehicle trea…
- GSE309348 Whole transcriptome sequencing of UPEC-infected testis and epididymis (5d) following depletion of CX3CR1+ macrophages 18 samples shares macrophage, depletion
- GSE288803 Proteasome inhibition alleviates proteinuria in Lmx1b knock-in mice with dysfunctional LIM domains 35 samples shares alleviates
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares macrophage
- GSE302019 Bulk RNA sequencing to investigate transcriptional profiles of lung macrophage subpopulations isolated from wild-type C57BL/6J and Spp1-EGFP knock-in reporter mice subjected to intratracheal administration of bleomycin or PBS. 24 samples shares macrophage
- GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares macrophage
- GSE179812 Macrophage Heterogeneity in Progression and Regression Phases of Cisplatin Induced AKI Mice Model - A single-cell RNA sequencing study 17 samples shares macrophage
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophage
- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares macrophage
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.