AP-1 mediated chromatin changes govern alveolar type 2 cell transition in lung injury-repair
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 14 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 GSE309751_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 PRJNA1336875 and SRA study SRP630195. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 6 as controls.
How we read this: Read from 14 sample titles: 14 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.
- GSM9278486 14 day mock PBS, AT2 cells, repliate 01, ATAC
- GSM9278487 14 day mock PBS, AT2 cells, repliate 02, ATAC
- GSM9278488 14 day SeV infected, AT2 cells, replicate 01, ATAC
- GSM9278489 14 day SeV infected, AT2 cells, replicate 02, ATAC
- GSM9278490 14 day SeV infected, AT2 cells, replicate 03, ATAC
- GSM9278491 49 day mock PBS, AT2 cells, repliate 01, ATAC
- GSM9278492 49 day mock PBS, AT2 cells, repliate 02, ATAC
- GSM9278493 49 day SeV infected, AT2 cells, replicate 01, ATAC
- GSM9278494 49 day SeV infected, AT2 cells, replicate 02, ATAC
- GSM9278495 KRAS negative control, AT2 cells, replicate 01, ATAC
- GSM9278496 KRAS negative control, AT2 cells, replicate 02, ATAC
- GSM9278497 KRAS induced, AT2 cells, replicate 01, ATAC
- GSM9278498 KRAS induced, AT2 cells, replicate 02, ATAC
- GSM9278499 KRAS induced, AT2 cells, replicate 03, ATAC
- GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares transition, chromatin
- GSE266022 Nrf2-mediated chromatin activation of hyperosmotic response genes attenuates heat-induced renal injury [ChIP-seq] 24 samples shares chromatin, mediated
- GSE246986 Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement 24 samples shares chromatin, mediated
- GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples shares chromatin, mediated
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares chromatin, mediated
- 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, changes
- 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
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.