Mechanotransduction mediated by cyclical respiratory motion maintains lung alveolar epithelial cell fate
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 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
- 11 samples: 2 × AT1, LB1, sample vs 2 × AT1, Input, sample vs 2 × AT2, LB1, sample vs 2 × AT2, Input, sampleGroups 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 GSE202319_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 PRJNA835452 and SRA study SRP373819. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 1 samples read as cases, 1 as controls.
How we read this: 4 replicated groups read from 11 sample titles; they account for 8 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.
- GSM6108299 Wildtype, scRNAseq
- GSM6108300 AT1_Cdc42 knockout, scRNAseq
- GSM6108301 Left bronchial ligation, scRNAseq
- GSM6108302 AT1, LB1, sample 1 AT1, LB1, sample
- GSM6108303 AT1, LB1, sample 2 AT1, LB1, sample
- GSM6108304 AT1, Input, sample 1 AT1, Input, sample
- GSM6108305 AT1, Input, sample 2 AT1, Input, sample
- GSM6108306 AT2, LB1, sample 1 AT2, LB1, sample
- GSM6108307 AT2, LB1, sample 2 AT2, LB1, sample
- GSM6108308 AT2, Input, sample 1 AT2, Input, sample
- GSM6108309 AT2, Input, sample 2 AT2, Input, sample
- GSE250359 PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [ATAC-seq] 11 samples shares epithelial, mediated, alveolar
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares epithelial, alveolar
- GSE287098 Influenza virus-induced type I interferons disrupt alveolar epithelial repair and tight junction integrity in the developing lung 96 samples shares epithelial, alveolar
- GSE271971 Pulmonary microvascular endothelial cells support alveolar epithelial growth via bone morphogenetic protein 6 secretion 72 samples shares epithelial, alveolar
- GSE271272 Fibroblast-derived osteoglycin promotes alveolar epithelial cell repair 32 samples shares epithelial, alveolar
- GSE306673 Akkermansia muciniphila contributes to fasting-mediated radioprotection by inducing epigenetic and transcriptional changes in small intestinal epithelial cells 32 samples shares epithelial, mediated
- GSE264369 Fatty acid oxidation downregulation in alveolar epithelial 2 cells promotes acute lung injury in obesity 18 samples shares epithelial, alveolar
- GSE273123 Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (Bulk RNA-Seq) 16 samples shares epithelial, alveolar
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.