Efferocytosis and other corpse clearance transfers metal micronutrients to engulfing macrophages triggering a metallothionein response necessary to preserve mitochondrial function
RNA-seq (gene expression) · mouse · 27 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
- 27 samples: 7 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.
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 GSE325042_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 PRJNA1438281 and SRA study SRP684273. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 27 samples.
How we read this: 7 replicated groups read from 27 sample titles; they account for 27 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.
- GSM9594575 non-engulfing, rep1 non-engulfing,
- GSM9594576 non-engulfing, rep2 non-engulfing,
- GSM9594577 non-engulfing, rep3 non-engulfing,
- GSM9594578 engulfing, rep1 engulfing,
- GSM9594579 engulfing, rep2 engulfing,
- GSM9594580 engulfing, rep3 engulfing,
- GSM9594581 control, rep1 control,
- GSM9594582 control, rep2 control,
- GSM9594583 control, rep3 control,
- GSM9635809 Recruited airway macrophages, non-engulfing, rep1 Recruited airway macrop…
- GSM9635810 Recruited airway macrophages, non-engulfing, rep2 Recruited airway macrop…
- GSM9635811 Recruited airway macrophages, non-engulfing, rep3 Recruited airway macrop…
- GSM9635812 Recruited airway macrophages, non-engulfing, rep4 Recruited airway macrop…
- GSM9635813 Recruited airway macrophages, engulfing, rep1 Recruited airway macrop…
- GSM9635814 Recruited airway macrophages, engulfing, rep2 Recruited airway macrop…
- GSM9635815 Recruited airway macrophages, engulfing, rep3 Recruited airway macrop…
- GSM9635816 Recruited airway macrophages, engulfing, rep4 Recruited airway macrop…
- GSM9635817 Resident airway macrophages, non-engulfing, rep1 Resident airway macroph…
- GSM9635818 Resident airway macrophages, non-engulfing, rep2 Resident airway macroph…
- GSM9635819 Resident airway macrophages, non-engulfing, rep3 Resident airway macroph…
- GSM9635820 Resident airway macrophages, non-engulfing, rep4 Resident airway macroph…
- GSM9635821 Resident airway macrophages, non-engulfing, rep5 Resident airway macroph…
- GSM9635822 Resident airway macrophages, engulfing, rep1 Resident airway macroph…
- GSM9635823 Resident airway macrophages, engulfing, rep2 Resident airway macroph…
- GSM9635824 Resident airway macrophages, engulfing, rep3 Resident airway macroph…
- GSM9635825 Resident airway macrophages, engulfing, rep4 Resident airway macroph…
- GSM9635826 Resident airway macrophages, engulfing, rep5 Resident airway macroph…
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares efferocytosis, macrophages
- GSE283547 Suppression of Notch during efferocytosis prevents macrophages inflammatory polarization [RNA-seq.HumanMouse] 40 samples shares efferocytosis, macrophages
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares mitochondrial, macrophages
- GSE279754 Cancer suppresses mitochondrial chaperone activity in macrophages to drive immune evasion 16 samples shares mitochondrial, macrophages
- GSE326335 Bulk RNA Sequencing of Chimera-Derived Monocyte-Derived Macrophages Targeted for Mitochondrial ROS During Peak Experimental Autoimmune Encephalomyelitis 14 samples shares mitochondrial, macrophages
- GSE245987 Vascular endothelial S1PR2 aggravates cardiac ischemia/reperfusion injury through triggering mitochondrial dysfunctions and endothelial pyroptosis via RHO/ROCK1/DRP1/NLRP3 pathway [heart] 4 samples shares mitochondrial, triggering
- GSE319375 Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [2] 18 samples shares efferocytosis, macrophages
- GSE306916 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages [ATAC-seq] 12 samples shares efferocytosis, macrophages
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.