Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 32 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
- 32 samples: 32 samples, each with a distinct title — no replicated groupsGroups 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
- Disease-associated astrocyte epigenetic memory promotes CNS pathologyNature · 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 GSE252551_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 PRJNA1061153 and SRA study SRP481649. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 32 sample titles: 32 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.
- GSM8003067 SPF_2X_Cytokine [ATAC_2_TAGGCATG]
- GSM8003068 SPF_2X_Cytokine [ATAC_2_CTCTCTAC]
- GSM8003069 SPF_2X_Cytokine [ATAC_2_CAGAGAGG]
- GSM8003070 SPF_2X_Cytokine [ATAC_2_GCTACGCT]
- GSM8003071 SPF_2X_Cytokine [ATAC_2_CGAGGCTG]
- GSM8003072 SPF_2X_PBS [ATAC_2_TAAGGCGA]
- GSM8003073 SPF_2X_PBS [ATAC_2_CGTACTAG]
- GSM8003074 SPF_2X_PBS [ATAC_2_AGGCAGAA]
- GSM8003075 SPF_2X_PBS [ATAC_2_TCCTGAGC]
- GSM8003076 SPF_2X_PBS [ATAC_2_GGACTCCT]
- GSM8148105 SPF 1X PBS_1 [RNA-Seq]
- GSM8148106 SPF 1X PBS_2 [RNA-Seq]
- GSM8148107 SPF 1X PBS_3 [RNA-Seq]
- GSM8148108 SPF 1X CYTOKINE_1 [RNA-Seq]
- GSM8148109 SPF 1X CYTOKINE_2 [RNA-Seq]
- GSM8148110 SPF 1X CYTOKINE_3 [RNA-Seq]
- GSM8148111 SPF 2X PBS_1 [RNA-Seq]
- GSM8148112 SPF 2X PBS_2 [RNA-Seq]
- GSM8148113 SPF 2X PBS_3 [RNA-Seq]
- GSM8148114 SPF 2X CYTOKINE_1 [RNA-Seq]
- GSM8148115 SPF 2X CYTOKINE_2 [RNA-Seq]
- GSM8148116 SPF 2X CYTOKINE_3 [RNA-Seq]
- GSM8148621 SPF_1X_Cytokine [ATAC_3_TAGGCATG]
- GSM8148622 SPF_1X_Cytokine [ATAC_3_CTCTCTAC]
- GSM8148623 SPF_1X_Cytokine [ATAC_3_CAGAGAGG]
- GSM8148624 SPF_1X_Cytokine [ATAC_3_GCTACGCT]
- GSM8148625 SPF_1X_Cytokine [ATAC_3_CGAGGCTG]
- GSM8148626 SPF_1X_PBS [ATAC_3_TAAGGCGA]
- GSM8148627 SPF_1X_PBS [ATAC_3_CGTACTAG]
- GSM8148628 SPF_1X_PBS [ATAC_3_AGGCAGAA]
- GSM8148629 SPF_1X_PBS [ATAC_3_TCCTGAGC]
- GSM8148630 SPF_1X_PBS [ATAC_3_GGACTCCT]
- GSE288348 Disease-associated astrocyte epigenetic memory promotes CNS pathology [sgEp300, sgACLY astrocytes bulk RNA-Seq dataset] 18 samples shares cns, disease-associated, epigenetic, astrocyte, pathology, promotes, rna-seq
- GSE325227 CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4+ T cells [RNA-seq_ATAC-seq] 22 samples shares epigenetic, atac-seq, rna-seq
- GSE332759 Intracellular complement factor H protects neurons during CNS inflammation [bulkRNA-seq] 16 samples shares cns, rna-seq
- GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares epigenetic, rna-seq
- GSE276155 RBBP5 is an epigenetic regulator of mammalian hepatic 12h oscillator [RNA-seq] 96 samples shares epigenetic, rna-seq
- GSE316619 Epigenetic memory of colitis promotes tumour growth 47 samples shares epigenetic, promotes
- GSE306262 Astrocyte glucocorticoid receptor signaling restricts neuronal plasticity [RNA-seq] 40 samples shares astrocyte, rna-seq
- GSE310017 Disease-associated mutations on the STAT5B SH2 domain regulate cholesterol and lipid metabolism in liver [RNA-Seq liver] 37 samples shares disease-associated, rna-seq
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.