Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage
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: 5 conditions, mostly in triplicateGroups 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
- Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in CartilageArthritis & rheumatology (Hoboken, N.J.) · 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 GSE230801_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 PRJNA962571 and SRA study SRP481307. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM7235228 ATAC_MAC_1 ATAC_MAC
- GSM7235229 ATAC_MAC_2 ATAC_MAC
- GSM7235230 ATAC_MAC_3 ATAC_MAC
- GSM7235237 MAC, siIRF1_1 MAC, siIRF1
- GSM7235238 MAC, siIRF1_2 MAC, siIRF1
- GSM7235239 MAC, siIRF1_3 MAC, siIRF1
- GSM7235240 MAC, siNC_1 MAC, siNC
- GSM7235241 MAC, siNC_2 MAC, siNC
- GSM7235242 MAC, siNC_3 MAC, siNC
- GSM8002344 Ad_Irf1_1 Ad_Irf1
- GSM8002345 Ad_Irf1_2 Ad_Irf1
- GSM8002346 Ad_Irf1_3 Ad_Irf1
- GSM8002347 Ad_eGFP_1 Ad_eGFP
- GSM8002348 Ad_eGFP_2 Ad_eGFP
- GSM8002349 Ad_eGFP_3 Ad_eGFP
- GSE228457 IL-7 mediated immunoregulatory feedback loop promotes dampening of immune effector functions by hypoinflammatory monocytes. 305 samples shares regulatory, promote
- GSE262131 Increased EZH2 function in regulatory T cells promotes their capacity to suppress autoimmunity by driving effector differentiation prior to activation. 36 samples shares regulatory, promote
- GSE213756 Serine enrichment in tumors promotes regulatory T cell accumulation through sphinganine mediated regulation of c-Fos 32 samples shares regulatory, promote
- GSE331248 Hepatic translation rewiring in insulin deficiency identifies Reg3α as an insulin-independent glucoregulatory factor [RNA_Ribo_Seq: ID_Healthy] 20 samples shares regulatory, deficiency
- GSE331062 Hepatic translation rewiring in insulin deficiency identifies Reg3α as an insulin-independent glucoregulatory factor 16 samples shares regulatory, deficiency
- GSE303194 Nano MiRNA-Functionating Tetrahedral Framework Nucleic Acid for Cartilage-targeted Ferritinophagy Modulation to Attenuate Temporomandibular Joint Osteoarthritis 15 samples shares osteoarthritis, cartilage
- GSE305276 Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone 9 samples shares osteoarthritis, cartilage
- GSE240635 Lysosomal control of type I interferon induction via Ragulator-Rag complex 48 samples shares interferon
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.