Whole-course Taming of Tumor-associated Macrophages from Central to Peripheral using Engineered Outer Membrane Vesicle Nanohybrids for Improved Immunotherapy [part 2: ATAC-seq]
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 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 GSE212260_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 PRJNA869176 and SRA study SRP394448. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM6520211 ATAC_GMPs_PBS_rep1 ATAC_GMPs_PBS
- GSM6520212 ATAC_GMPs_PBS_rep2 ATAC_GMPs_PBS
- GSM6520213 ATAC_GMPs_PBS_rep3 ATAC_GMPs_PBS
- GSM6520214 ATAC_GMPs_OMV-SIRP_rep1 ATAC_GMPs_OMV-SIRP
- GSM6520215 ATAC_GMPs_OMV-SIRP_rep2 ATAC_GMPs_OMV-SIRP
- GSM6520217 ATAC_GMPs_OMV-SIRP_rep3 ATAC_GMPs_OMV-SIRP
- GSM6520218 ATAC_GMPs_OMV-SIRP-G_rep1 ATAC_GMPs_OMV-SIRP-G
- GSM6520219 ATAC_GMPs_OMV-SIRP-G_rep2 ATAC_GMPs_OMV-SIRP-G
- GSM6520220 ATAC_GMPs_OMV-SIRP-G_rep3 ATAC_GMPs_OMV-SIRP-G
- GSM6520221 ATAC_Monos_PBS_rep1 ATAC_Monos_PBS
- GSM6520222 ATAC_Monos_PBS_rep2 ATAC_Monos_PBS
- GSM6520224 ATAC_Monos_PBS_rep3 ATAC_Monos_PBS
- GSM6520225 ATAC_Monos_OMV-SIRP_rep1 ATAC_Monos_OMV-SIRP
- GSM6520226 ATAC_Monos_OMV-SIRP_rep2 ATAC_Monos_OMV-SIRP
- GSM6520227 ATAC_Monos_OMV-SIRP_rep3 ATAC_Monos_OMV-SIRP
- GSM6520228 ATAC_Monos_OMV-SIRP-G_rep1 ATAC_Monos_OMV-SIRP-G
- GSM6520229 ATAC_Monos_OMV-SIRP-G_rep2 ATAC_Monos_OMV-SIRP-G
- GSM6520231 ATAC_Monos_OMV-SIRP-G_rep3 ATAC_Monos_OMV-SIRP-G
- GSE290434 A stress response axis in tumor-associated macrophages dictates phenotype heterogeneity and immunotherapy evasion 21 samples shares tumor-associated, immunotherapy, macrophages
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares tumor-associated, macrophages, engineered
- GSE306916 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages [ATAC-seq] 12 samples shares tumor-associated, macrophages
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares tumor-associated, macrophages
- GSE237783 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages [RNA-Seq] 28 samples shares tumor-associated, macrophages
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares tumor-associated, macrophages
- GSE285794 Cancer cell-derived arginine fuels polyamine biosynthesis in tumor-associated macrophages to promote immune evasion 12 samples shares tumor-associated, macrophages
- GSE271267 Tumoral Interferon Beta Induces an Immune-Stimulatory Phenotype in Tumor-Associated Macrophages in Melanoma Brain Metastases 12 samples shares tumor-associated, 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.