Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 64 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
- 64 samples: 19 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
- Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1Nature neuroscience · 2024
Read the full summary ↓
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 GSE208742_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 PRJNA860940 and SRA study SRP387431. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 2 as controls.
How we read this: 19 replicated groups read from 64 sample titles; they account for 48 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.
- GSM6368705 Multiome_scRNA-seq_Astro
- GSM6368706 Multiome_scRNA-seq_GFP
- GSM6368707 Multiome_scRNA-seq_Ngn2
- GSM6368708 Multiome_scRNA-seq_PmutNgn2
- GSM6368709 Multiome_scATAC-seq_Astro
- GSM6368710 Multiome_scATAC-seq_GFP
- GSM6368711 Multiome_scATAC-seq_Ngn2
- GSM6368712 Multiome_scATAC-seq_PmutNgn2
- GSM6368713 Bulk RNA-seq GFP rep1 Bulk RNA-seq GFP
- GSM6368714 Bulk RNA-seq GFP rep2 Bulk RNA-seq GFP
- GSM6368715 Bulk RNA-seq GFP rep3 Bulk RNA-seq GFP
- GSM6368716 Bulk RNA-seq Ngn2 rep1 Bulk RNA-seq Ngn2
- GSM6368717 Bulk RNA-seq Ngn2 rep2 Bulk RNA-seq Ngn2
- GSM6368718 Bulk RNA-seq Ngn2 rep3 Bulk RNA-seq Ngn2
- GSM6368719 Bulk RNA-seq PmutNgn2 rep1 Bulk RNA-seq PmutNgn2
- GSM6368720 Bulk RNA-seq PmutNgn2 rep2 Bulk RNA-seq PmutNgn2
- GSM6368721 Bulk RNA-seq PmutNgn2 rep3 Bulk RNA-seq PmutNgn2
- GSM6368722 Bulk ATAC-seq GFP rep1 Bulk ATAC-seq GFP
- GSM6368723 Bulk ATAC-seq GFP rep2 Bulk ATAC-seq GFP
- GSM6368724 Bulk ATAC-seq GFP rep3 Bulk ATAC-seq GFP
- GSM6368725 Bulk ATAC-seq Ngn2 rep1 Bulk ATAC-seq Ngn2
- GSM6368726 Bulk ATAC-seq Ngn2 rep2 Bulk ATAC-seq Ngn2
- GSM6368727 Bulk ATAC-seq Ngn2 rep3 Bulk ATAC-seq Ngn2
- GSM6368728 Bulk ATAC-seq PmutNgn2 rep1 Bulk ATAC-seq PmutNgn2
- GSM6368729 Bulk ATAC-seq PmutNgn2 rep2 Bulk ATAC-seq PmutNgn2
- GSM6368730 Bulk ATAC-seq PmutNgn2 rep3 Bulk ATAC-seq PmutNgn2
- GSM6368731 Methyl-HiC GFP rep1 Methyl-HiC GFP
- GSM6368732 Methyl-HiC GFP rep2 Methyl-HiC GFP
- GSM6368733 Methyl-HiC GFP rep3 Methyl-HiC GFP
- GSM6368734 Methyl-HiC Ngn2 rep1 Methyl-HiC Ngn2
- GSM6368735 Methyl-HiC Ngn2 rep2 Methyl-HiC Ngn2
- GSM6368736 Methyl-HiC PmutNgn2 rep1 Methyl-HiC PmutNgn2
- GSM6368737 Methyl-HiC PmutNgn2 rep2 Methyl-HiC PmutNgn2
- GSM6368738 ChIP-seq Ngn2 rep1 ChIP-seq Ngn2
- GSM6368739 ChIP-seq Ngn2 rep2 ChIP-seq Ngn2
- GSM6368740 ChIP-seq Ngn2 rep3 ChIP-seq Ngn2
- GSM6368741 ChIP-seq Input rep1 ChIP-seq Input
- GSM6368742 ChIP-seq Input rep2 ChIP-seq Input
- GSM6368743 ChIP-seq Input rep3 ChIP-seq Input
- GSM6368744 Yy1_scRNAseq_gene_expression_library
+ 24 more — browse all 64 samples with per-sample file links →
- GSE267452 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming 54 samples shares reprogramming, direct
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares reprogramming, remodeling
- GSE294521 Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG] 34 samples shares remodeling, direct
- GSE305453 Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivo 15 samples shares reprogramming, direct
- GSE306458 ACVR1-mediated glycolytic reprogramming promotes histone lactylation and neuronal pyroptosis in neuropathic pain {ChIP-seq] 12 samples shares reprogramming, neuronal
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares remodeling
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares remodeling
- GSE237954 Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer 122 samples shares reprogramming
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.