Multi-omics approaches for identification of novel dynamic regulators in transcriptional landscape and chromatin accessibility changes in liver regeneration and hepatocyte organoid formation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
- 27 samples: 10 conditions, mostly in duplicateGroups 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 GSE243402_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 PRJNA1018424 and SRA study SRP460715. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 27 sample titles; they account for 20 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.
- GSM7783003 Undamaged_Tissue [ATAC-seq]
- GSM7783004 PHx_6h_Tissue [ATAC-seq]
- GSM7783005 PHx_12h_Tissue [ATAC-seq]
- GSM7783006 PHx_24h_Tissue [ATAC-seq]
- GSM7783007 PHx_48h_Tissue [ATAC-seq]
- GSM7783008 Hep_Org_P0_4d [ATAC-seq]
- GSM7783009 Hep_Org_P1_6d [ATAC-seq]
- GSM7783012 Undamaged_control_rep1 Undamaged_control
- GSM7783013 Undamaged_control_rep2 Undamaged_control
- GSM7783014 PHx_6h_1 PHx_6h
- GSM7783015 PHx_12h_1 PHx_12h
- GSM7783016 PHx_24h_1 PHx_24h
- GSM7783017 PHx_48h_1 PHx_48h
- GSM7783018 PHx_72h_1 PHx_72h
- GSM7783019 PHx_7d_1 PHx_7d
- GSM7783020 PHx_14d_1 PHx_14d
- GSM7783021 PHx_21d_1 PHx_21d
- GSM7783022 Hep_Orgs_rep1 Hep_Orgs
- GSM7783023 Hep_Orgs_rep2 Hep_Orgs
- GSM8844919 PHx_6h_2 PHx_6h
- GSM8844920 PHx_12h_2 PHx_12h
- GSM8844921 PHx_24h_2 PHx_24h
- GSM8844922 PHx_48h_2 PHx_48h
- GSM8844923 PHx_72h_2 PHx_72h
- GSM8844924 PHx_7d_2 PHx_7d
- GSM8844925 PHx_14d_2 PHx_14d
- GSM8844926 PHx_21d_2 PHx_21d
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares accessibility, chromatin
- GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares regeneration, hepatocyte
- GSE156569 BRG1 contributes to the global chromatin accessibility revealed by its acute depletion 102 samples shares accessibility, chromatin
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares accessibility, chromatin
- GSE296014 Post-replicative chromatin accessibility predicts cell fate change. 81 samples shares accessibility, chromatin
- GSE216371 A single-cell atlas of chromatin accessibility in mouse organogenesis 68 samples shares accessibility, chromatin
- GSE309545 Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD-associated kinase LRRK2 between human and mice [multiome mouse] 64 samples shares accessibility, chromatin
- GSE240860 Hmgb2 improves astrocyte to neuron conversion by increasing the chromatin accessibility of genes associated with neuronal maturation in a proneuronal factor-dependent manner 54 samples shares accessibility, 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.