Epigenetic modification, as a distinctive therapeutic molecule for Parkinson’s disease gene therapy.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 17 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
- 17 samples: 13 distinct titles, 4 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.
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 GSE308116_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 PRJNA1328757 and SRA study SRP620539. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 17 sample titles: 13 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.
- GSM9238106 Mouse, sham, rep1
- GSM9238107 Mouse, sham, rep2
- GSM9238108 Mouse, 6-OHDA, rep1
- GSM9238109 Mouse, 6-OHDA+NDST3, rep1
- GSM9238110 Mouse, 6-OHDA+NDST3, rep2
- GSM9238111 Mouse, H3K27ac, sham, rep1
- GSM9238112 Mouse, H3K27ac,sham, rep2
- GSM9238113 Mouse, H3K27ac,6-OHDA, rep1
- GSM9238114 Mouse, H3K27ac,6-OHDA, rep2
- GSM9238115 Mouse, H3K27ac,6-OHDA+NDST3, rep1
- GSM9238116 Mouse, H3K27ac,6-OHDA+NDST3, rep2
- GSM9238117 Mouse, ATAC, sham
- GSM9238118 Mouse, ATAC, 6-OHDA
- GSM9238119 Mouse, ATAC, 6-OHDA+NDST3
- GSM9238120 Mouse, scRNA, sham
- GSM9238121 Mouse, scRNA, 6-OHDA
- GSM9238122 Mouse, scRNA, 6-OHDA+NDST3
- GSE274865 Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [CUT&Tag] 36 samples shares epigenetic, therapy
- GSE278517 Telomere recapping via gene therapy as a therapeutic strategy for cardio-renal syndromes type 4 12 samples shares therapeutic, therapy
- GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares epigenetic
- GSE292063 Pre-existing epigenetic state and differential NF-kB activation shape type 2 immune cell responses 61 samples shares epigenetic
- GSE288348 Disease-associated astrocyte epigenetic memory promotes CNS pathology [sgEp300, sgACLY astrocytes bulk RNA-Seq dataset] 18 samples shares epigenetic
- GSE327604 Epigenetic control of microglial mitochondrial immunity by KAT7 drives Alzheimer’s disease pathogenesis [RNA-Seq] 12 samples shares epigenetic
- GSE202694 The transcriptional factor ONECUT3 is a driver and therapeutic target for complex karyotype MDS 12 samples shares therapeutic
- GSE300019 The CARM1 Epigenetic Enzyme Inhibits Cross-presenting Dendritic Cell Function in Cancer Immunity [multiome] 8 samples shares epigenetic
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.