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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell RNAseq of control chimeric mouse embryos at embryonic days 7.5 and 8.5 of mouse development

ABSTRACT: Chimeric mouse embryos were generated as a control experiment to understand the contribution of host vs. injected cells to the developing embryo. Embryos were generated by blastocyst injection of tdTomato-labelled mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Carolina Guibentif

PROVIDER: E-MTAB-7324 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A single-cell molecular map of mouse gastrulation and early organogenesis.

Pijuan-Sala Blanca B Griffiths Jonathan A JA Guibentif Carolina C Hiscock Tom W TW Jawaid Wajid W Calero-Nieto Fernando J FJ Mulas Carla C Ibarra-Soria Ximena X Tyser Richard C V RCV Ho Debbie Lee Lian DLL Reik Wolf W Srinivas Shankar S Simons Benjamin D BD Nichols Jennifer J Marioni John C JC Göttgens Berthold B

Nature 20190220 7745

Across the animal kingdom, gastrulation represents a key developmental event during which embryonic pluripotent cells diversify into lineage-specific precursors that will generate the adult organism. Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization. We construct a molecular map of cellular differentiation from pluripotency towards all major embryonic lineages, and explor ...[more]

PMID: 30787436

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Single-cell RNAseq of additional control chimeric mouse embryos at embryonic day 8.5 of mouse development

Project description:This dataset contains additional data performed as in the experiment stored at accession E-MTAB-7324. Chimeric mouse embryos were generated as a control experiment to understand the contribution of host vs. injected cells to the developing embryo. Embryos were generated by blastocyst injection of tdTomato-labelled mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2020-08-31 | E-MTAB-8812 | biostudies-arrayexpress

Single-cell RNAseq of Tal1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development

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Single-cell RNAseq of Tal1 knockout chimeric mouse embryos at embryonic days 7.5 and 8.5 of mouse development.

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Single-cell RNAseq of Brachyury knockout chimeric mouse embryos at embryonic days 8.5 and 7.5 of mouse development.

Project description:Chimeric embryos were generated to investigate the effect of T knockout in mouse embryos by single-cell RNA-sequencing. T is an essential transcription factor for axial embryonic patterning. Chimeric embryos contain tissue that is T+/+, which prevents global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Tal1-/- mouse embryonic stem cells into wild type embryos. After blastocyst harvest, cells were flow-sorted before 10X Genomics library preparation and single-cell RNA-sequencing.

2020-08-31 | E-MTAB-8811 | biostudies-arrayexpress

Single-cell RNAseq of Mixl1 knockout chimeric mouse embryos at embryonic day 8.5 of mouse development.

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NPKLH data

Project description:Comparison of the germinal center B cell receptor repertoire in Cxcl13-Cre/TdTom EYFP (control) and Cxcl13-Cre/TdTom EYFP Cxcl12fl/fl mice on day following subcutaneous immunization with NP-KLH.

2020-05-12 | E-MTAB-8904 | biostudies-arrayexpress

Single-cell gene expression of germinal center B cells from CXCL12-conditionally deficient and –sufficient mice

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2020-05-12 | E-MTAB-8454 | biostudies-arrayexpress

Single-cell gene expression of lymph node B cell-interacting reticular cells

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2020-05-12 | E-MTAB-8445 | biostudies-arrayexpress

Cellular plasticity and diversity during heart valve epithelial-to-mesenchymal transitions revealed using single-cell RNA-seq

Project description:We have generated scRNA-seq data from embryonic day (E)10.5 and E12.5 atrioventricular canals (primitive heart valves) to assess cellular diversity during the distinct epithelial-to-mesenchymal transitions (EMTs) from endocardium and epicardium that guide the formation of valve mesenchyme. Alongside, wildtype atrioventricular canals, we generated scRNA-seq data from Sox9 conditional knockouts (Sox9fl/fl;Tie2-cre) to explore the role of SOX9 in EMT. Atrioventricular canals were microdissected from cardiac chambers and outflow tract, enriching for heart valve progenitor lineages.

2023-06-30 | E-MTAB-11795 | biostudies-arrayexpress

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Project description:The tumor microenvironment (TME) is a complex mixture of tumor cells, immune cells, endothelial cells and fibroblastic stroma cells (FSC). While cancer-associated fibroblasts are generally seen as a tumor-promoting entity, it is conceivable that distinct FSC populations within the TME contribute to immune-mediated tumor control. Here, we show that intra-tumoral injection of a recombinant LCMV-based vaccine vector (r3LCMV) expressing the melanocyte differentiation antigen TRP2 results in T cell-dependent eradication of melanomas. Analysis of the TME revealed that viral vector transduction precipitates activation of particular FSC subsets. Using single-cell RNA-seq analysis, we identified a Cxcl13-expressing FSC population with a pronounced immune-stimulatory signature and increased expression of the inflammatory cytokine IL-33. Genetic ablation of Il33 in Cxcl13-Cre+ FSC impeded functionality of intratumoral T cells and consequently tumor control. Thus, reprogramming of distinct FSC subsets in the TME through LCMV-based vectors efficiently promotes tumor eradication by locally sustaining the activity of tumor-specific T cells.

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