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
Single-cell RNA-seq · mouse · 39 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 39 samples: 39 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.
- Paper
- Early-stage lung cancer is driven by a transitional cell state dependent on a KRAS-ITGA3-SRC axisThe EMBO journal · 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 GSE253461_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 PRJNA1065850 and SRA study SRP484209. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 39 sample titles: 39 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.
- GSM8020962 Freshly sorted Y AT2 cells, no Ad-Cre treatment
- GSM8020963 Freshly sorted KPY AT2 cells, no Ad-Cre treatment
- GSM8020964 In vitro mesenchymal cells before co-culturing with organoids
- GSM8020965 Y AT2 organoids, 4 days after Ad5CMV-Cre
- GSM8020966 Mesenchymal cells co-cultured with Y organoids, 4 days
- GSM8020967 KPY AT2 organoids, 4 days after Ad5CMV-Cre
- GSM8020968 Mesenchymal cells co-cultured with KPY organoids, 4 days
- GSM8020969 Y AT2 organoids, 7 days after Ad5CMV-Cre
- GSM8020970 Mesenchymal cells co-cultured with Y organoids, 7 days
- GSM8020971 KPY AT2 organoids, 7 days after Ad5CMV-Cre
- GSM8020972 Mesenchymal cells co-cultured with KPY organoids, 7 days
- GSM8020973 Y AT2 organoids, 10 days after Ad5CMV-Cre
- GSM8020974 Mesenchymal cells co-cultured with Y organoids, 10 days
- GSM8020975 KPY AT2 organoids, 10 days after Ad5CMV-Cre
- GSM8020976 Mesenchymal cells co-cultured with KPY organoids, 10 days
- GSM8020977 Y AT2 organoids, 14 days after Ad5CMV-Cre
- GSM8020978 Mesenchymal cells co-cultured with Y organoids, 14 days
- GSM8020979 KPY AT2 organoids, 14 days after Ad5CMV-Cre
- GSM8020980 Mesenchymal cells co-cultured with KPY organoids, 14 days
- GSM8020981 AT2 YFP+ cells, 4 weeks after Ad5SPC-Cre
- GSM8020982 Mesenchymal cells, 4 weeks after Ad5SPC-Cre
- GSM8020983 Endothelial cells, 4 weeks after Ad5SPC-Cre
- GSM8020984 Immune cells, 4 weeks after Ad5SPC-Cre
- GSM8020985 AT2 YFP+ cells, 7 weeks after Ad5SPC-Cre
- GSM8020986 Mesenchymal cells, 7 weeks after Ad5SPC-Cre
- GSM8020987 Endothelial cells, 7 weeks after Ad5SPC-Cre
- GSM8020988 Immune cells, 7 weeks after Ad5SPC-Cre
- GSM8020989 AT2 YFP+ cells, 10 weeks after Ad5SPC-Cre
- GSM8020990 Mesenchymal cells, 10 weeks after Ad5SPC-Cre
- GSM8020991 Endothelial cells, 10 weeks after Ad5SPC-Cre
- GSM8020992 Immune cells, 10 weeks after Ad5SPC-Cre
- GSM8020993 AT2 YFP+ cells, 16 weeks after Ad5SPC-Cre
- GSM8020994 Mesenchymal cells, 16 weeks after Ad5SPC-Cre
- GSM8020995 Endothelial cells, 16 weeks after Ad5SPC-Cre
- GSM8020996 Immune cells, 16 weeks after Ad5SPC-Cre
- GSM8020997 Control (YFP GEMM) AT2 cells, 4 weeks after Ad5SPC-Cre
- GSM8020998 Control (YFP GEMM) Mesenchymal cells, 4 weeks after Ad5SPC-Cre
- GSM8020999 Control (YFP GEMM) Endothelial cells, 4 weeks after Ad5SPC-Cre
- GSM8021000 Control (YFP GEMM) Immune cells, 4 weeks after Ad5SPC-Cre
- GSE320248 Single-cell sequencing study of splenocytes and YFP+ B cells to investigate differences between Eif3e cg1cre knockout mice and control mice 8 samples shares yfp, single-cell
- GSE276257 Single-cell transcriptomics of Smad4fl/fl and Smad4fl/fl;Rosa26-creERT2 (Smad4iko) mice. 7 samples shares rosa26, single-cell
- GSE313553 Single-cell transcriptomic profiling of c-Kit⁺ HSPCs in a KrasG12D/+ mouse model of JMML 2 samples shares g12d, single-cell
- GSE123064 Single-cell transcriptomics of spinal microglia from Cx3cr1-Cre-YFP x flxRunx1 mice 2 samples shares yfp, single-cell
- GSE272843 A single-cell atlas of normal and KRASG12D-malformed lymphatic vessels 2 samples shares g12d, single-cell
- GSE81903 Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP X Thy1-stop-YFP Line#1 mice 384 samples shares yfp
- GSE233452 Fractionation of sgControl, sgIfih1 and sgGgnbp2 in HoxA9 immortalized Rosa26-CreERT2 Adar1fl/E861A immortalised myeloid cells. 54 samples shares rosa26
- GSE312064 Ascertaining the effect of switching deregulated Myc OFF in KRasG12D/MycER-driven mouse lung tumors 32 samples shares g12d
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.