Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunity [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 15 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
- 15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
- Endogenous glucocorticoids are required for normal macrophage activation and gastric Helicobacter pylori immunityAmerican journal of physiology. Gastrointestinal and liver physiology · 2024
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 GSE253583_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 PRJNA1066314 and SRA study SRP484558. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 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.
- GSM8023854 GD387-Busada_ATAC_WT
- GSM8023855 GD388-Busada_ATAC_WT
- GSM8023856 GD389-Busada_ATAC_WT
- GSM8023857 GD390-Busada_ATAC_WT
- GSM8023858 GD391-Busada_ATAC_KO
- GSM8023859 GD392-Busada_ATAC_KO
- GSM8023860 GD393-Busada_ATAC_KO
- GSM8023861 GD394-Busada_ATAC_WT
- GSM8023862 GD395-Busada_ATAC_WT
- GSM8023863 GD396-Busada_ATAC_WT
- GSM8023864 GD397-Busada_ATAC_WT
- GSM8023865 GD398-Busada_ATAC_KO
- GSM8023866 GD399-Busada_ATAC_KO
- GSM8023867 GD400-Busada_ATAC_KO
- GSM8023868 GD401-Busada_ATAC_KO
- GSE245646 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ATAC-seq_muscle] 22 samples shares macrophage, activation, atac-seq
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares endogenous, macrophage, immunity
- GSE280514 Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair. 48 samples shares macrophage, required
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophage, activation
- GSE327645 BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq] 28 samples shares macrophage, atac-seq
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares macrophage, immunity
- GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares macrophage, activation
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.