GEO series
Mapping the Dialogue: Decoding Alveolar Stem-Niche Interactions [I]
GSE307112
Mus musculus; Homo sapiens
Expression profiling by high throughput sequencing
886 samples
Submitted 2026/06/29
Platform GPL35012
Summary
Cellular atlases reveal diverse cellular phenotypes, but how cells traverse this phenotypic landscape to impact tissues requires systematic study. We present an alveolosphere screening platform for investigating interactions between lung epithelial stem cells and their fibroblast niche. We assessed the role of 201 candidate genes in stem cells via imaging, then used RNAseq analysis for a transcriptome-wide understanding of cell-autonomous effects on stem cells and non-cell-autonomous effects on the niche. This phenome-transcriptome map uncovered new cellular states and pathways regulating stem cell growth, metabolism, and immune signaling. Notably, stem cells influenced scar-forming and immune programs in fibroblasts. This injury response was dependent on stem cell identity; loss of Nkx2.1, the transcription factor conferring lung epithelial identity, disrupted stem cell-niche interactions and had a greater non-cell-autonomous effect than eliminating the cancer genes Trp53, Egfr, or Cdkn2b. Our study highlights how functional atlases complement the cellular diversity revealed by descriptive methods.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE307112_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 886 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1314575 and SRA study SRP616810. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 886 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9215859 lung alveolar organoid, Met knockout, plate1-1 well B02
- GSM9215860 lung alveolar organoid, Glis3 knockout, plate1-1 well B03
- GSM9215861 lung alveolar organoid, Tigit knockout, plate1-1 well B04
- GSM9215862 lung alveolar organoid, Tdtomato knockout, plate1-1 well B05
- GSM9215863 lung alveolar organoid, Trp53 knockout, plate1-1 well B06
- GSM9215864 lung alveolar organoid, Acp6 knockout, plate1-1 well B07
- GSM9215865 lung alveolar organoid, Pink1 knockout, plate1-1 well B08
- GSM9215866 lung alveolar organoid, Eif2ak3 knockout, plate1-1 well B09
- GSM9215867 lung alveolar organoid, Ccbe1 knockout, plate1-1 well B10
- GSM9215868 lung alveolar organoid, Gdf2 knockout, plate1-1 well B11
- GSM9215869 lung alveolar organoid, Tead1 knockout, plate1-1 well C02
- GSM9215870 lung alveolar organoid, Mecom knockout, plate1-1 well C03
- GSM9215871 lung alveolar organoid, Huwe1 knockout, plate1-1 well C04
- GSM9215872 lung alveolar organoid, Sftpd knockout, plate1-1 well C05
- GSM9215873 lung alveolar organoid, Trp63 knockout, plate1-1 well C06
- GSM9215874 lung alveolar organoid, Il1a knockout, plate1-1 well C07
- GSM9215875 lung alveolar organoid, Prkn knockout, plate1-1 well C08
- GSM9215876 lung alveolar organoid, Tigit knockout, plate1-1 well C09
- GSM9215877 lung alveolar organoid, Bmp10 knockout, plate1-1 well C10
- GSM9215878 lung alveolar organoid, Pla2g15 knockout, plate1-1 well C11
- GSM9215879 lung alveolar organoid, Ror1 knockout, plate1-1 well D02
- GSM9215880 lung alveolar organoid, Npnt knockout, plate1-1 well D03
- GSM9215881 lung alveolar organoid, Rnf43 knockout, plate1-1 well D04
- GSM9215882 lung alveolar organoid, Tns1 knockout, plate1-1 well D05
- GSM9215883 lung alveolar organoid, Ttf1 knockout, plate1-1 well D06
- GSM9215884 lung alveolar organoid, Tigit knockout, plate1-1 well D07
- GSM9215885 lung alveolar organoid, Keap1 knockout, plate1-1 well D08
- GSM9215886 lung alveolar organoid, Tfeb knockout, plate1-1 well D09
- GSM9215887 lung alveolar organoid, Fgf7 knockout, plate1-1 well D10
- GSM9215888 lung alveolar organoid, Il1a knockout, plate1-1 well D11
- GSM9215889 lung alveolar organoid, Tfcp2l1 knockout, plate1-1 well E02
- GSM9215890 lung alveolar organoid, Tigit knockout, plate1-1 well E03
- GSM9215891 lung alveolar organoid, Sox4 knockout, plate1-1 well E04
- GSM9215892 lung alveolar organoid, Twist1 knockout, plate1-1 well E05
- GSM9215893 lung alveolar organoid, Nkx21 knockout, plate1-1 well E06
- GSM9215894 lung alveolar organoid, Usp30 knockout, plate1-1 well E07
- GSM9215895 lung alveolar organoid, Nfe2l2 knockout, plate1-1 well E08
- GSM9215896 lung alveolar organoid, Ulk1 knockout, plate1-1 well E09
- GSM9215897 lung alveolar organoid, Inhba knockout, plate1-1 well E10
- GSM9215898 lung alveolar organoid, Manf knockout, plate1-1 well E11
+ 846 more — browse all 886 samples with per-sample file links →
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