Endothelial Cells retain inflammatory memory through chromatin remodeling [ATAC]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 3 × Clp_Sp vs 3 × Clp_Saline vs 3 × Sham_Saline vs 3 × Sham_SpGroups 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
- Endothelial cells retain inflammatory memory through chromatin remodeling in a two-hit model of infection-induced inflammationAmerican journal of physiology. Cell physiology · 2025
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 GSE301784_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 PRJNA1287566 and SRA study SRP599054. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9089619 Clp_Sp_Rep1 Clp_Sp
- GSM9089620 Clp_Saline_Rep2 Clp_Saline
- GSM9089621 Sham_Saline_Rep3 Sham_Saline
- GSM9089622 Sham_Sp_Rep4 Sham_Sp
- GSM9089623 Clp_Saline_Rep5 Clp_Saline
- GSM9089624 Clp_Sp_Rep6 Clp_Sp
- GSM9089625 Sham_Sp_Rep7 Sham_Sp
- GSM9089626 Sham_Saline_Rep8 Sham_Saline
- GSM9089627 Clp_Sp_Rep9 Clp_Sp
- GSM9089628 Sham_Sp_Rep10 Sham_Sp
- GSM9089629 Clp_Saline_Rep11 Clp_Saline
- GSM9089630 Sham_Saline_Rep12 Sham_Saline
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares endothelial, remodeling, chromatin, retain, memory
- GSE236575 Adipose tissue retains an epigenetic memory of obesity after weight loss [ATAC-seq] 22 samples shares atac, retain, memory
- GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples shares atac, remodeling, chromatin
- GSE342565 Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq 2 samples shares atac, endothelial, chromatin
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares atac, chromatin
- GSE294103 SIRT6 Overexpression Counteracts Chromatin Aging [ATAC-Seq_tg] 28 samples shares atac, chromatin
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares atac, memory
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares atac, 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.