Vascularized Macrophage-Islet Organoids to Model Immune-Mediated Pancreatic beta cell Pyroptosis upon Viral Infection
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 22 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
- Homo sapiens (human)
- Samples
- 22 samples: 17 distinct titles, 3 of them repeatedGroups 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.
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 GSE247809_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 PRJNA1040752 and SRA study SRP472011. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 10 as controls.
How we read this: Read from 22 sample titles: 17 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.
- GSM7901006 unstimulated hESC-derived macrophages-1
- GSM7901007 unstimulated hESC-derived macrophages-2
- GSM7901008 unstimulated hESC-derived macrophages-3
- GSM7901009 Stimulated hESC-derived macrophages-1
- GSM7901010 Stimulated hESC-derived macrophages-2
- GSM7901011 Stimulated hESC-derived macrophages-3
- GSM7901012 control-9-mock
- GSM7901013 control-9-SARS-CoV-2
- GSM7901014 control-10-mock
- GSM7901015 control-10-SARS-CoV-2
- GSM7901016 control-10-CVB4
- GSM7901017 control-11-mock
- GSM7901018 control-11-SARS-CoV-2
- GSM7901019 control-12-mock
- GSM7901020 control-12-CVB4-1
- GSM7901021 control-12-CVB4-2
- GSM7901022 non-coculture cells (Separately cultured cells)-RNA
- GSM7901023 VMI organoids with unstimulated macrophages-RNA
- GSM7901024 VMI organoids with pro-inflammatory macrophages-RNA
- GSM7901025 non-coculture cells (Separately cultured cells)-ATAC
- GSM7901026 VMI organoids with unstimulated macrophages-ATAC
- GSM7901027 VMI organoids with pro-inflammatory macrophages-ATAC
- GSE272460 Transcriptome analysis of pancreatic progenitor organoids (POs) carrying PDAC related mutations, treated with ERK inhibitors and depleted of AP-1 factors 40 samples shares pancreatic, organoids
- GSE263364 Characterization of human pancreatic tissue and organoids reveals subpopulation of intercalated duct cells with progenitor traits 23 samples shares pancreatic, organoids
- GSE228801 Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction 14 samples shares pancreatic, organoids
- GSE275610 scRNA-seq and snATAC-seq reveal differentiation trajectories of several pancreatic islet induction protocols 341 samples shares pancreatic
- GSE285406 ZNF274 constrains lineage plasticity and drives intrinsic resistance to CDK7 inhibitors in pancreatic cancer 48 samples shares pancreatic
- GSE335464 Integrative single-cell multi-omics profiling of human pancreatic islets identifies T1D-associated genes and regulatory signals [single cell] 28 samples shares pancreatic
- GSE300200 The Lysine Demethylase Kdm4C is an Oncogenic Driver and Regulates ERK Activity in KRAS Mutant Pancreatic Ductal Adenocarcinoma 26 samples shares pancreatic
- GSE300595 Multiomic sequencing identifies myeloid cell associations with neoadjuvant chemotherapy treatment response in pancreatic adenocarcinoma (PDAC) 24 samples shares pancreatic
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.