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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: Chimeric embryos were generated to investigate the effect of Tal1 knockout in mouse embryos by single-cell RNA-sequencing. Tal1 is an essential transcription factor for the formation of the embryonic blood. Embryo chimerism permits the analysis of the effects of Tal1 knockout without the confounding effects of the absence of embryonic blood, which results in 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.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Jonathan Griffiths

PROVIDER: E-MTAB-7325 | 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

Similar Datasets

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

Project description:Chimeric embryos were generated to investigate the effect of Tal1 knockout in mouse embryos by single-cell RNA-sequencing. Tal1 is an essential transcription factor for the formation of the embryonic blood. Embryo chimerism permits the analysis of the effects of Tal1 knockout without the confounding effects of the absence of embryonic blood, which results in 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.

2018-12-05 | E-MTAB-6968 | biostudies-arrayexpress

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

Project description: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.

2018-12-05 | E-MTAB-7324 | biostudies-arrayexpress

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 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.

Project description:Chimeric embryos were generated to investigate the effect of Mixl1 knockout in mouse embryos by single-cell RNA-sequencing. Mixl1 is an essential transcription factor for mesendoderm development. Chimeric embryos contain tissue that is Mixl1+/+, which prevents global developmental failures. Embryos were generated by blastocyst injection of tdTomato-labelled, Mixl1-/- 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.

2023-10-26 | E-MTAB-13409 | biostudies-arrayexpress

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

Project description:Efficient germinal center formation requires the coordinated movement of B cells between distinct regions of the B cell follicle where their fate and function is governed by the integration of cues from their interacting partners. While CXCL13 is known to be important for B cell chemoattraction and follicle formation, the molecular identity of B cell-interacting reticular cells remains ill-defined. Moreover, how CXCL13-expressing, B-cell interacting reticular cells are reprogramed to cater to the developing germinal center remains unclear. Here we use the Cxcl13-Cre/TdTomato mouse model to genetically target and decipher the cellular composition of lymph node CXCL13-expressing reticular cells under steady-state and inflammatory conditions. Moreover, we examine the consequence of cell-specific, genetic perturbation of CXCL12 on the molecular identity of the reticular cell network. Transcriptomic analyses revealed that B cell follicle reticular cell subset specification is predetermined in the steady-state, although additional transcriptional changes accompany germinal center formation. Although genetic perturbation of CXCL12 alters GC topology, the molecular identity of the underlying reticular cells remains largely unperturbed.

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

Identification of cell surface markers and establishment of monolayer differentiation protocol for retinal pigment epithelial cells.

Project description:In vitro differentiation of human pluripotent stem cells into functional retinal pigment epithelial (RPE) cells for cell based reparative therapy of age-related macular degeneration (AMD). In the present study, we identify CD140b, CD56, GD2 and CD184 as central cell surface markers to evaluate hPSC-RPE differentiation efficiency, as well as a potential tool for the enrichment of hPSC-RPE during and after differentiation. Using these markers together with single cell RNA sequencing to evaluate the differentiation process, we have established an efficient xeno-free and defined monolayer differentiation methodology where culture on supportive human recombinant laminin eliminates the need for manual selection, allowing large-scale production of pure hPSC-RPE.

2020-02-29 | E-MTAB-7742 | biostudies-arrayexpress

Single-cell transcriptomics reveals early emergence of liver parenchymal and non-parenchymal cell lineages

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