AP-1 mediated chromatin changes govern alveolar type 2 cell transition in lung injury-repair [multiome]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 8 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
- 8 samples: 8 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.
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 GSE310539_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 PRJNA1366485 and SRA study SRP648394. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 4 as controls.
How we read this: Read from 8 sample titles: 8 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.
- GSM9303242 Multiome, wildtype PBS control lung epithelial cells, GEX
- GSM9303243 Multiome, wildtype PBS control lung epithelial cells, ATAC
- GSM9303244 Multiome, wildtype SeV infected lung epithelial cells, GEX
- GSM9303245 Multiome, wildtype SeV infected lung epithelial cells, ATAC
- GSM9303246 Multiome, AP-1 mut PBS control lung epithelial cells, GEX
- GSM9303247 Multiome, AP-1 mut PBS control lung epithelial cells, ATAC
- GSM9303248 Multiome, AP-1 mutant SeV infected lung epithelial cells, GEX
- GSM9303249 Multiome, AP-1 mutant SeV infected lung epithelial cells, ATAC
- GSE333887 Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [transplantations_OneCell_multiome] 14 samples shares transition, chromatin, multiome
- 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 chromatin, multiome, changes
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares chromatin, multiome
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares transition, chromatin
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares chromatin, mediated
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares chromatin, mediated
- GSE266024 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury 42 samples shares chromatin, mediated
- GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares chromatin, mediated
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.