Macrophages sense ECM mechanics and growth factor availability through cytoskeletal remodeling to regulate their tissue repair program
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: 6 conditions, mostly in duplicateGroups 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
- Mechanosensing regulates tissue repair program in macrophagesScience advances · 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 GSE239378_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 PRJNA998930 and SRA study SRP451646. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 12 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.
- GSM7661246 BMDMs, Petri_Untx_1
- GSM7661247 BMDMs, Petri_IL_4_2
- GSM7661248 BMDMs, Petri_Untx_DMSO_3
- GSM7661249 BMDMs, Petri_IL_4_DMSO_4
- GSM7661250 BMDMs, Petri_IL_4_LatA_6
- GSM7661251 BMDMs, Petri_IL_4_MCSF_10
- GSM7663870 BMDMs, TC_Untx_24hrs_13 BMDMs, TC_Untx_24hrs
- GSM7663871 BMDMs, TC_Untx_24hrs_14 BMDMs, TC_Untx_24hrs
- GSM7663872 BMDMs, TC_IL-4_24hrs_15 BMDMs, TC_IL-4_24hrs
- GSM7663873 BMDMs, TC_IL-4_24hrs_16 BMDMs, TC_IL-4_24hrs
- GSM7663874 BMDMs, 7mg_Untx_24hrs_17 BMDMs, 7mg_Untx_24hrs
- GSM7663875 BMDMs, 7mg_Untx_24hrs_18 BMDMs, 7mg_Untx_24hrs
- GSM7663876 BMDMs, 7mg_IL-4_24hrs_19 BMDMs, 7mg_IL-4_24hrs
- GSM7663877 BMDMs, 7mg_IL-4_24hrs_20 BMDMs, 7mg_IL-4_24hrs
- GSM7663878 BMDMs, 2mg_Untx_24hrs_21 BMDMs, 2mg_Untx_24hrs
- GSM7663879 BMDMs, 2mg_Untx_24hrs_22 BMDMs, 2mg_Untx_24hrs
- GSM7663880 BMDMs, 2mg_IL-4_24hrs_23 BMDMs, 2mg_IL-4_24hrs
- GSM7663881 BMDMs, 2mg_IL-4_24hrs_24 BMDMs, 2mg_IL-4_24hrs
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares macrophages, regulate, program
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages, remodeling
- GSE253848 Mechano-oncogenic cytoskeletal remodeling drives leukemic transformation with mitochondrial vesicle-mediated STING activation 54 samples shares cytoskeletal, remodeling
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares macrophages, program
- 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 macrophages, program
- GSE243269 The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages 12 samples shares macrophages, regulate
- GSE325061 Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis 12 samples shares macrophages, regulate
- GSE231992 Diet-induced obesity dysregulates rapid epigenetic response to hypoxia in macrophages (RNA-Seq) 12 samples shares macrophages, regulate
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.