Cohesin complex cooperates with PU.1 at super-enhancers to regulate the differentiation and identity of conventional dendritic cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 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
- 34 samples: 17 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.
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 GSE326309_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 PRJNA1445099 and SRA study SRP687697. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 34 samples.
How we read this: 17 replicated groups read from 34 sample titles; they account for 34 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.
- GSM9628921 cDC_WT1 cDC_WT
- GSM9628922 cDC_WT2 cDC_WT
- GSM9628923 cDC_KO1 cDC_KO
- GSM9628924 cDC_KO2 cDC_KO
- GSM9628925 pDC_WT1 pDC_WT
- GSM9628926 pDC_WT2 pDC_WT
- GSM9628927 pDC_KO1 pDC_KO
- GSM9628928 pDC_KO2 pDC_KO
- GSM9628929 preDC_WT1 preDC_WT
- GSM9628930 preDC_WT2 preDC_WT
- GSM9628931 preDC_KO1 preDC_KO
- GSM9628932 preDC_KO2 preDC_KO
- GSM9628933 SMC1A_cDC_WT1 SMC1A_cDC_WT
- GSM9628934 SMC1A_cDC_WT2 SMC1A_cDC_WT
- GSM9628935 SMC1A_cDC_KO1 SMC1A_cDC_KO
- GSM9628936 SMC1A_cDC_KO2 SMC1A_cDC_KO
- GSM9628937 PU1_cDC_WT1 PU1_cDC_WT
- GSM9628938 PU1_cDC_WT2 PU1_cDC_WT
- GSM9628939 PU1_cDC_KO1 PU1_cDC_KO
- GSM9628940 PU1_cDC_KO2 PU1_cDC_KO
- GSM9628941 H3K27Ac_cDC_WT1 H3K27Ac_cDC_WT
- GSM9628942 H3K27Ac_cDC_WT2 H3K27Ac_cDC_WT
- GSM9628943 H3K27Ac_cDC_KO1 H3K27Ac_cDC_KO
- GSM9628944 H3K27Ac_cDC_KO2 H3K27Ac_cDC_KO
- GSM9628945 Input_cDC_WT1 Input_cDC_WT
- GSM9628946 Input_cDC_WT2 Input_cDC_WT
- GSM9628947 HiC_cDC_WT1 HiC_cDC_WT
- GSM9628948 HiC_cDC_WT2 HiC_cDC_WT
- GSM9628949 HiC_cDC_KO1 HiC_cDC_KO
- GSM9628950 HiC_cDC_KO2 HiC_cDC_KO
- GSM9628951 scRNAseq_WT1 scRNAseq_WT
- GSM9628952 scRNAseq_WT2 scRNAseq_WT
- GSM9628953 scRNAseq_KO1 scRNAseq_KO
- GSM9628954 scRNAseq_KO2 scRNAseq_KO
- GSE271298 Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells 103 samples shares dendritic, cohesin
- GSE263078 The histone demethylase KDM5C regulates IRF transcriptional programming impacting dendritic cell population heterogeneity and function 67 samples shares dendritic, regulate
- GSE276024 Mitochondrial metabolism regulates the immunogenic responsiveness of dendritic cells [RNA-seq] 24 samples shares dendritic, regulate
- GSE288378 Dendritic cells regulate the innate-adaptive balance in lymph nodes for optimal host defense 24 samples shares dendritic, regulate
- GSE264053 Dysregulated innate immune signaling cooperates with RUNX1 mutations to transform an MDS-like disease to AML 24 samples shares cooperates, regulate
- GSE314783 Phagocytosis of necroptotic cells optimizes type 1 conventional dendritic cells for induction of a cytotoxic T-cell response 17 samples shares conventional, dendritic
- GSE280985 An immunobiliary single-cell atlas resolves crosstalk between type 2 conventional dendritic cells and γδ T cells in cholangitis [scRNA-seq] 14 samples shares conventional, dendritic
- GSE269588 Plekhg5 regulates the unconventional secretion of Sod1 by presynaptic secretory autophagy 12 samples shares conventional, 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.