Organoid modeling of lung branching morphogenesis and epithelial lineage specification [RNA-Seq]
Single-cell RNA-seq · mouse · 40 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 40 samples: 33 distinct titles, 5 of them repeatedGroups 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 GSE300722_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1281906 and SRA study SRP594494. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 40 sample titles: 33 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.
- GSM9067318 LO_day8
- GSM9067319 LO_day11
- GSM9067320 LO_day18
- GSM9067321 LO_day11_DCI
- GSM9067324 down-half (2)
- GSM9067325 down-half-left (7)
- GSM9067326 down-half-right (8)
- GSM9067327 intact(0)
- GSM9067328 left-half (3)
- GSM9067329 right-half (4)
- GSM9067330 up-half (1)
- GSM9067331 up-half-left (5)
- GSM9067332 up-half-right (6)
- GSM9067333 E10.5_Tip
- GSM9067334 E11.5_Tip
- GSM9067335 E12.5_Tip
- GSM9067336 E13.5_Tip
- GSM9067337 organoid_E10.5_11d
- GSM9067338 organoid_E10.5_18d
- GSM9067339 organoid_E10.5_32d
- GSM9067340 organoid_E11.5_11d
- GSM9067341 organoid_E13.5_11d
- GSM9067342 organoid_E13.5_19d
- GSM9067343 organoid_E13.5_30d
- GSM9067345 organoid_E14_11d
- GSM9067347 organoid_E14_24d
- GSM9067349 organoid_E9.5_13d
- GSM9477004 2C
- GSM9477005 2C+F10
- GSM9477006 2C+MTG
- GSM9477007 2C+VC
- GSM9477008 ALL
- GSM9477009 ALL_r1
- GSM9477010 ALL_r2
- GSM9477011 ALL-FGF10_r1
- GSM9477012 ALL-FGF10_r2
- GSM9477013 ALL-MTG_r1
- GSM9477014 ALL-MTG_r2
- GSM9477015 ALL-VC_r1
- GSM9477016 ALL-VC_r2
- GSE303739 Organoid modeling of lung branching morphogenesis and epithelial lineage specification 56 samples shares morphogenesis, specification, epithelial, branching, organoid, modeling, lineage
- GSE269973 Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [RNA-Seq] 32 samples shares epithelial, organoid, rna-seq
- GSE273123 Aberrant Transitional Alveolar Epithelial Cells Promote Pathogenic Activation of Lung Fibroblasts in Preclinical Fibrosis Modeling (Bulk RNA-Seq) 16 samples shares epithelial, modeling, rna-seq
- GSE307773 Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq] 175 samples shares epithelial, rna-seq
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares epithelial, rna-seq
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares epithelial, rna-seq
- 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, organoid
- GSE272476 Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [RNA-seq] 30 samples shares epithelial, rna-seq
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.