Autoimmune inflammation triggers an HSC-derived trained immunity program in myeloid cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 54 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
- 54 samples: 48 distinct titles, 6 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.
- Paper
- A distinct metabolic and epigenetic state drives trained immunity in HSC-derived macrophages from autoimmune miceCell stem cell · 2024
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 GSE215004_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 PRJNA888060 and SRA study SRP379111. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 54 sample titles: 48 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.
- GSM6213395 GMP, Control, replicate 1
- GSM6213396 GMP, Control, replicate 2
- GSM6213397 GMP, Pristane, replicate 1
- GSM6213398 GMP, Pristane, replicate 2
- GSM6619867 GMP, Control, Replicate 1 [Con_GMP_1]
- GSM6619868 GMP, Control, Replicate 2 [Con_GMP_2]
- GSM6619869 GMP, Control, Replicate 3 [Con_GMP_3]
- GSM6619870 GMP, Pristane, Replicate 1 [Lup_GMP_1]
- GSM6619871 GMP, Pristane, Replicate 2 [Lup_GMP_2]
- GSM6619872 GMP, Pristane, Replicate 3 [Lup_GMP_3]
- GSM6619873 GMP, Control, replicate 1 [control_GMP_1]
- GSM6619874 GMP, Control, replicate 2 [control_GMP_2]
- GSM6619875 GMP, Control, replicate 3 [control_GMP_3]
- GSM6619876 SLAM, Control, replicate 1 [control_HSC_1]
- GSM6619877 SLAM, Control, replicate 2 [control_HSC_2]
- GSM6619878 SLAM, Control, replicate 3 [control_HSC_3]
- GSM6619879 BM Mon, Control, replicate 1 [control_monocyte_1]
- GSM6619880 BM Mon, Control, replicate 2 [control_monocyte_2]
- GSM6619881 BM Mon, Control, replicate 3 [control_monocyte_3]
- GSM6619882 MPPG/M, Control, replicate 1 [control_MPP3_1]
- GSM6619883 MPPG/M, Control, replicate 2 [control_MPP3_2]
- GSM6619884 MPPG/M, Control, replicate 3 [control_MPP3_3]
- GSM6619885 GMP, Pristane, replicate 1 [lupus_GMP_1]
- GSM6619886 GMP, Pristane, replicate 2 [lupus_GMP_2]
- GSM6619887 GMP, Pristane, replicate 3 [lupus_GMP_3]
- GSM6619888 SLAM, Pristane, replicate 1 [lupus_HSC_1]
- GSM6619889 SLAM, Pristane, replicate 2 [lupus_HSC_2]
- GSM6619890 SLAM, Pristane, replicate 3 [lupus_HSC_3]
- GSM6619891 BM Mon, Pristane, replicate 1 [lupus_monocyte_1]
- GSM6619892 BM Mon, Pristane, replicate 2 [lupus_monocyte_2]
- GSM6619893 BM Mon, Pristane, replicate 3 [lupus_monocyte_3]
- GSM6619894 MPPG/M, Pristane, replicate 1 [lupus_MPP3_1]
- GSM6619895 MPPG/M, Pristane, replicate 2 [lupus_MPP3_2]
- GSM6619896 MPPG/M, Pristane, replicate 3 [lupus_MPP3_3]
- GSM8267746 primary, BMDM, Control, replicate 1
- GSM8267749 primary, BMDM, Control, replicate 2
- GSM8267751 primary, BMDM, Pristane, replicate 1
- GSM8267753 primary, BMDM, Pristane, replicate 2
- GSM8267818 transplant-derived, BMDM, Control, replicate 1
- GSM8267819 transplant-derived, BMDM, Control, replicate 2
+ 14 more — browse all 54 samples with per-sample file links →
- GSE288114 Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [RNA-Seq] 32 samples shares immunity, program
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares immunity, program
- GSE295483 Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages [RNA-seq] 19 samples shares immunity, trained
- GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares triggers, program
- GSE306371 Unconventional role of HMGCS1 in driving pathogenic-Th17 cell immunity and autoimmune diseases 16 samples shares autoimmune, immunity
- GSE252949 Cell surface-targeted immunocytokines program systemic anti-tumor immunity 15 samples shares immunity, program
- GSE270414 Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Bulk RNA-seq CTNNB1/hMet/NFE2L2] 13 samples shares immunity, program
- GSE296733 Elevated Ozone Activates Maternal Immunity to Drive Offspring IgG-Mediated Anaphylaxis through IgG Glycosylation Reprogramming 12 samples shares immunity, program
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.