Identifying a perivascular niche supporting lung alveoli epithelial stem cells and metastatic cancer cells
RNA-seq (gene expression) · mouse · 17 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 17 samples: 6 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
- Characterization of perivascular alveolar epithelial stem cells and their niche in lung homeostasis and cancerStem cell reports · 2024
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 GSE183152_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA759276 and SRA study SRP333939. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 6 replicated groups read from 17 sample titles; they account for 17 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.
- GSM5534837 AT2 cells, CD44hi_1 AT2 cells, CD44hi
- GSM5534838 AT2 cells, CD44hi_2 AT2 cells, CD44hi
- GSM5534839 AT2 cells, CD44hi_3 AT2 cells, CD44hi
- GSM5534840 AT2 cells, CD44lo_1 AT2 cells, CD44lo
- GSM5534841 AT2 cells, CD44lo_2 AT2 cells, CD44lo
- GSM5534842 AT2 cells, CD44lo_3 AT2 cells, CD44lo
- GSM8262790 nonPA CD44hi_1 nonPA CD44hi
- GSM8262791 nonPA CD44hi_2 nonPA CD44hi
- GSM8262792 3d PA CD44loSca1- _1 3d PA CD44loSca1
- GSM8262793 3d PA CD44loSca1+ _ 1 3d PA CD44loSca1+
- GSM8262794 3d PA CD44hi _1 3d PA CD44hi
- GSM8262795 3d PA CD44loSca1- _2 3d PA CD44loSca1
- GSM8262796 3d PA CD44loSca1+ _ 2 3d PA CD44loSca1+
- GSM8262797 3d PA CD44hi _2 3d PA CD44hi
- GSM8262798 3d PA CD44loSca1- _3 3d PA CD44loSca1
- GSM8262799 3d PA CD44loSca1+ _ 3 3d PA CD44loSca1+
- GSM8262800 3d PA CD44hi _3 3d PA CD44hi
- 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, lung
- GSE287098 Influenza virus-induced type I interferons disrupt alveolar epithelial repair and tight junction integrity in the developing lung 96 samples shares epithelial, lung
- GSE303739 Organoid modeling of lung branching morphogenesis and epithelial lineage specification 56 samples shares epithelial, lung
- GSE300722 Organoid modeling of lung branching morphogenesis and epithelial lineage specification [RNA-Seq] 40 samples shares epithelial, lung
- GSE253461 Single-cell transcriptional profiling of wildtype Rosa26(YFP) (Y) and Kras(G12D) p53(-/-) Rosa26-YFP (KPY) lung AT2 epithelial cells, AT2 organoids, and co-cultured mesenchymal cells with temporal resolution 39 samples shares epithelial, lung
- GSE330206 Effects of NTHi on lung epithelial regeneration mechanisms in mouse-derived air-liquid interface cultures 23 samples shares epithelial, lung
- GSE264369 Fatty acid oxidation downregulation in alveolar epithelial 2 cells promotes acute lung injury in obesity 18 samples shares epithelial, lung
- GSE249931 Temporal single-cell profiling of distinct mesenchymal, epithelial, endothelial, and immune cell lineages in the lung after injury 17 samples shares epithelial, lung
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.