Intestinal plasmacytoid dendritic cells preferentially produce interferon lambda
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 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
- 11 samples: 4 × Gut vs 4 × SpleenGroups 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
- Plasmacytoid dendritic cells in the intestine preferentially produce interferon lambda at homeostasis contributing to tonic localized innate immune responsesbioRxiv : the preprint server for biology · 2025
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 GSE304886_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 PRJNA1303150 and SRA study SRP607444. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 2 replicated groups read from 11 sample titles; they account for 8 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.
- GSM9158990 Gut_1 Gut
- GSM9158991 Gut_2 Gut
- GSM9158992 Gut_3 Gut
- GSM9158993 Gut_4 Gut
- GSM9158994 Spleen_1 Spleen
- GSM9158995 Spleen_2 Spleen
- GSM9158996 Spleen_3 Spleen
- GSM9158997 Spleen_4 Spleen
- GSM9158998 pool1_GEX
- GSM9158999 pool1_HTO
- GSM9159000 pool1_ADT
- GSE252188 Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells [Bulk RNA-seq] 15 samples shares plasmacytoid, interferon, dendritic
- GSE296433 Engineered probiotics limit T-cell driven CNS autoimmunity by activating AHR-KLF4-FADS3 signaling in intestinal dendritic cells 40 samples shares intestinal, dendritic
- GSE302271 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 2] 22 samples shares plasmacytoid, dendritic
- GSE302124 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1] 18 samples shares plasmacytoid, dendritic
- GSE247149 Type III interferons induce pyroptosis in gut epithelial cells and delay tissue restitution upon acute intestinal injury. 16 samples shares intestinal, interferon
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares intestinal
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares intestinal
- GSE288156 Progressive intestinal tumor cell plasticity, Myc activation and loss of Lgr5+ tumor stem cell lineage commitment upon Wnt depletion 14 samples shares intestinal
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.