Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [2]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 15 distinct titles, 3 of them repeatedGroups 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.
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 GSE319375_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 PRJNA1423170 and SRA study SRP676747. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 sample titles: 15 distinct titles with little repetition. 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.
- GSM7255610 NaiveBasalRep1
- GSM7255611 NaiveBasalRep2
- GSM7255612 TrainedBasalRep1
- GSM7255613 TrainedBasalRep2
- GSM7255616 Control Alveolar Macrophage Rep1 Batch1 [ABM1]
- GSM7255618 7day LPS AM Rep1 Batch1 [ABM2]
- GSM7255619 72h LPS AM Rep1 Batch1 [ABM3]
- GSM7255620 7day72h LPS AM Rep1 Batch1 [ABM4]
- GSM7255621 Control Alveolar Macrophage Rep2 Batch2 [ABM13]
- GSM7255622 7day LPS AM Rep2 Batch2 [ABM14]
- GSM7255623 72h LPS AM Rep2 Batch2 [ABM15]
- GSM7255624 7day72h LPS AM Rep2 Batch2 [ABM16]
- GSM7255626 Control Alveolar Macrophage Rep3 Batch3 [ABM25]
- GSM7255627 7day LPS AM Rep3 Batch3 [ABM26]
- GSM7255628 72h LPS AM Rep3 Batch3 [ABM27]
- GSM7255629 7day72h LPS AM Rep3 Batch3 [ABM28]
- GSM9516734 72h post-LPS Rep1
- GSM9516735 72h post-LPS Rep2
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, alveolar, promotes
- GSE295483 Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [RNA-seq] 19 samples shares macrophages, immunity, alveolar
- GSE281001 The C3-C3aR axis modulates trained immunity in alveolar macrophages 8 samples shares macrophages, immunity, alveolar
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares macrophages, alveolar
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares efferocytosis, macrophages
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophages, promotes
- GSE303772 Ontogenically distinct alveolar macrophages mediate cigarette smoke-induced inflammation and damage [RNA-Seq] 24 samples shares macrophages, alveolar
- GSE210798 Splenic CD169+Tim4+ Marginal Zone Metallophilic Macrophages Are Essential for Wound Healing and Resolution of Inflammation After Myocardial Infarction 24 samples shares macrophages, resolution
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.