Pulmonary alveoli are complex architectural units thought to undergo endogenous or pharmacologically induced programs of regeneration and degeneration. To study the molecular mechanism of alveoli loss mice were calorie restricted at different timepoints. Lungs were harvested and processed for RNA extraction.
Calorie-related rapid onset of alveolar loss, regeneration, and changes in mouse lung gene expression.
Time
View SamplesIt has been shown that dexamethasone (Dex) impairs the normal lung septation that occurs in the early postnatal period. Treatment with retinoic acid (ATRA) abrogates the effects of Dex. To understand the molecular basis for the Dex indiced inhibition of the formation of the alveoli and the ability of ATRA to prevent the inhibition of septation, gene expression was analyzed in 4-day old mice treated with diluent (control), Dex-treated and ATRA+Dex-treated.
DNA microarray analysis of neonatal mouse lung connects regulation of KDR with dexamethasone-induced inhibition of alveolar formation.
No sample metadata fields
View SamplesThe mammalian liver consists of hexagonal-shaped lobules, radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labor has not been achieved. Here we measure the whole transcriptome of thousands of single mouse liver cells and infer their lobule coordinates using a panel of zonated landmark genes, characterized with single-molecule FISH. We obtain a genome-wide reconstruction of liver zonation profiles with unprecedented spatial resolution. We find that more than 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. Our approach can facilitate reconstruction of similar spatial genomic blueprints for other mammalian organs. Overall design: mRNA profiles from single cells extracted from mouse liver were generated by deep sequencing of 1736 of single cells, sequenced in several batches in an Illumina NextSeq.
Single-cell spatial reconstruction reveals global division of labour in the mammalian liver.
Cell line, Subject
View SamplesForkhead box class O (FoxO) transcription factors regulate whole body energy metabolism, skeletal muscle mass and substrate switching. To elucidate the role of FOXO in skeletal muscle, dominant negative (dn) constructs for FOXO1 (FOXO1dn) or FOXO3 (FOXO3dn) were transfected by electroporation into mouse tibialis anterior muscle and glucose uptake, signal transduction, and glucose stimulated gene expression profiles were assessed. Results were compared against contralateral control transfected muscle.
Regulation of glucose uptake and inflammation markers by FOXO1 and FOXO3 in skeletal muscle.
Sex, Age, Specimen part
View SamplesIdentification of genes that are involved in self-seeding by comparing gene expression profiles between parental MDA-MB-231 cells and seeder cells (MDA-231-S1a and S1b)
Tumor self-seeding by circulating cancer cells.
No sample metadata fields
View SamplesComparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.
Latent bone metastasis in breast cancer tied to Src-dependent survival signals.
No sample metadata fields
View SamplesComparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.
Latent bone metastasis in breast cancer tied to Src-dependent survival signals.
No sample metadata fields
View SamplesComparisons among breast cancer metastases at different organs revealed distinct microenvironments as characterized by cytokine content.
Latent bone metastasis in breast cancer tied to Src-dependent survival signals.
No sample metadata fields
View SamplesMetastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with unprecedented sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert fluorocytosine to fluorouracil, covalently labeling nascent RNA for purification and sequencing. Flura-seq revealed that breast cancer micrometastases in lung and brain exhibit unique, reversible gene signatures depending on the microenvironment. Specifically, the mitochondrial electron transport Complex I and the NRF2-driven antioxidant programs were induced in oxygen-rich pulmonary micrometastases, compared to mammary tumors or brain micrometastases. Loss of Complex I activity, and antioxidant supplementation potentiated pulmonary metastatic growth. We confirm lung metastasis-specific NRF2 overexpression in clinical samples, thus validating Flura-seq's utility in identifying clinically actionable microenvironmental adaptations in early metastasis. The sensitivity, robustness and economy of Flura-seq are broadly applicable beyond cancer research. Overall design: Examination of 5-FU labeled RNAs in cancer cells present in different organs
Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization.
Cell line, Subject
View SamplesIdentify Wnt3A responsive signature in lung adenocarcinoma cells
WNT/TCF signaling through LEF1 and HOXB9 mediates lung adenocarcinoma metastasis.
No sample metadata fields
View Samples