cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 33 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
- 33 samples: 5 × Lung primary fibroblasts, cGAS KO, female vs 5 × Lung primary fibroblasts, cGAS KO, male vs 5 × Lung primary fibroblasts, WT, male vs 4 × Lung primary fibroblasts, WT, femaleGroups 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 GSE279026_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 PRJNA1169945 and SRA study SRP675196. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 19 samples.
How we read this: 4 replicated groups read from 33 sample titles; they account for 19 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.
- GSM8559734 Lung primary fibroblasts, cGAS KO, female 1 Lung primary fibroblast…
- GSM8559735 Lung primary fibroblasts, cGAS KO, female 2 Lung primary fibroblast…
- GSM8559736 Lung primary fibroblasts, cGAS KO, male 1 Lung primary fibroblast…
- GSM8559737 Lung primary fibroblasts, cGAS KO, male 2 Lung primary fibroblast…
- GSM8559738 Lung primary fibroblasts, WT, female 1 Lung primary fibroblast…
- GSM8559739 Lung primary fibroblasts, WT, female 2 Lung primary fibroblast…
- GSM8559740 Lung primary fibroblasts, WT, male 1 Lung primary fibroblast…
- GSM8559741 Lung primary fibroblasts, WT, male 2 Lung primary fibroblast…
- GSM8559742 Lung primary fibroblasts, cGAS KO, female 1 Lung primary fibroblast…
- GSM8559743 Lung primary fibroblasts, cGAS KO, female 2 Lung primary fibroblast…
- GSM8559744 Lung primary fibroblasts, cGAS KO, female 3 Lung primary fibroblast…
- GSM8559745 Lung primary fibroblasts, cGAS KO, male 1 Lung primary fibroblast…
- GSM8559746 Lung primary fibroblasts, cGAS KO, male 2 Lung primary fibroblast…
- GSM8559747 Lung primary fibroblasts, cGAS KO, male 3 Lung primary fibroblast…
- GSM8559748 Lung primary fibroblasts, WT, female 1 Lung primary fibroblast…
- GSM8559749 Lung primary fibroblasts, WT, female 2 Lung primary fibroblast…
- GSM8559750 Lung primary fibroblasts, WT, male 1 Lung primary fibroblast…
- GSM8559751 Lung primary fibroblasts, WT, male 2 Lung primary fibroblast…
- GSM8559752 Lung primary fibroblasts, WT, male 3 Lung primary fibroblast…
- GSM9500710 Lung primary fibroblasts, cGAS KO, female 1, h3k27me3
- GSM9500711 Lung primary fibroblasts, cGAS KO, female 1, h3k9me3
- GSM9500712 Lung primary fibroblasts, cGAS KO, female 2, h3k27me3
- GSM9500713 Lung primary fibroblasts, cGAS KO, female 2, h3k9me3
- GSM9500714 Lung primary fibroblasts, cGAS KO, female 3, h3k27me3
- GSM9500715 Lung primary fibroblasts, cGAS KO, female 3, h3k9me3
- GSM9500716 Lung primary fibroblasts, cGAS KO, female 3, IgG
- GSM9500717 Lung primary fibroblasts, WT, female 1, h3k27me3
- GSM9500718 Lung primary fibroblasts, WT, female 1, h3k9me3
- GSM9500719 Lung primary fibroblasts, WT, female 2, h3k27me3
- GSM9500720 Lung primary fibroblasts, WT, female 2, h3k9me3
- GSM9500721 Lung primary fibroblasts, WT, female 3, h3k27me3
- GSM9500722 Lung primary fibroblasts, WT, female 3, h3k9me3
- GSM9500723 Lung primary fibroblasts, WT, female 3, IgG
- GSE279025 cGAS deficient mice display premature aging associated with loss of chromatin organization, derepression of LINE1 elements and induction of inflammation [RNA-seq] 11 samples shares line1, organization, derepression, deficient, premature, chromatin, induction, elements
- GSE309572 MLL2 facilitates long-range gene regulation through LINE1 elements [ChIP-Seq] 89 samples shares line1, elements
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares organization, chromatin
- GSE271298 Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells 103 samples shares organization, chromatin
- GSE204933 Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice 82 samples shares organization, chromatin
- GSE214438 Age-associated chromatin re-organization in progenitor B cells 76 samples shares organization, chromatin
- GSE287375 CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq] 54 samples shares organization, chromatin
- GSE284165 Reorganization of PBAF/cBAF remodelers on H3.3 chromatin regulates BMAL1 activity in the absence of circadian negative feedback 47 samples shares organization, chromatin
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.