Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNAseq of whole B6 mouse E8.25 embryos

ABSTRACT: Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~20000 cells from C57BL/6 E8.25 mouse embryos.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Wajid Jawaid

PROVIDER: E-MTAB-6153 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

Ibarra-Soria Ximena X Jawaid Wajid W Pijuan-Sala Blanca B Ladopoulos Vasileios V Scialdone Antonio A Jörg David J DJ Tyser Richard C V RCV Calero-Nieto Fernando J FJ Mulas Carla C Nichols Jennifer J Vallier Ludovic L Srinivas Shankar S Simons Benjamin D BD Göttgens Berthold B Marioni John C JC

Nature cell biology 20180108 2

During gastrulation, cell types from all three germ layers are specified and the basic body plan is established <sup>1</sup> . However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems <sup>2</sup> . Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 ...[more]

PMID: 29311656

Similar Datasets

Single-cell RNAseq of whole mouse E8.25 embryos

Project description:Gastrulation represents a pivotal point in mammalian development, when the basic body plan is established and cells are specified into one of the three germ layers. This is followed by rapid diversification into specific lineages and the appearance of the various cell types required to build each of the organs. The rich variety of cell types present at this stage has never been rigorously characterised in any mammalian organism, and thus insight into cell fate decisions and the underlying regulatory networks have been inaccessible. We have used droplet based single-cell RNA-sequencing to address this by profiling ~7000 cells from three E8.25 mouse embryos.

2017-12-01 | E-MTAB-5728 | biostudies-arrayexpress

Timecourse single-cell RNAseq of whole mouse embryos harvested between days 6.5 and 8.5 of development.

Project description:We have captured 100,000 single cells for single-cell RNAseq from whole mouse embryos during gastrulation and organogenesis, spanning days 6.5 to 8.5 of development, including embryonic and extraembryonic tissues. Cells were sampled every six hours, providing a continuous molecular characterisation of these processes. Cell libraries were prepared using the 10X Genomics Chromium platform.

2018-12-05 | E-MTAB-6967 | 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

Tracking Early Mammalian Organogenesis – Prediction and Validation of Differentiation Trajectories at Whole Organism Scale

Project description:This project is based on the extension of the single cell transcriptomics atlas of mouse development towards E9.5. Inference of cell differentiation trajectories was carried out using Waddington-Optimal Transport, and the resulting computational reconstruction was contrasted with grafting experiments as well as complementary scRNA-seq experiments.

2023-01-01 | E-MTAB-11763 | biostudies-arrayexpress

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

Project description:To characterize the heterogeneity within endothelial, mesenchymal, and hepatic lineages through formation of the embryonic mouse liver bud, we have performed single-cell RNA sequencing on mouse embryos, spanning days 9.5 to 10.5 of development. This data set includes 12,470 cells with a mean detected gene number of 4,588.

2020-10-29 | E-MTAB-9334 | biostudies-arrayexpress

A high-resolution single-cell multiomic atlas of the human fetal lung - scRNA / GEX / VDJ

Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.

2022-01-27 | E-MTAB-11278 | biostudies-arrayexpress

RNA-seq from human peripheral blood isolated and CRISPR/Cas9-mediated BCL11B depleted alpha-beta CD8+ T cells and corresponding not transfected (nt) and mock (mock gRNA transfected) controls.

Project description:B-cell lymphoma/leukemia (BCL) 11B represents a major regulator of vital processes in post-thymic lymphocytes as well as of lymphocyte differentiation by blocking NK cell and promoting T cell development and is thus considered a \\"guardian of T cell fate\\". Interestingly, on the one hand, NK cell maturation correlates with increased expression of BCL11B, on the other hand, native or induced T cell populations characterized by multiple NK cell features showed reduced BCL11B expression. Both NK cells or T cells display unique and desired features for cellular therapies. NK cells are able to efficiently lyse cancerous or virally infected cells but can only be poorly expanded in vitro. In contrast, T cell cytotoxic activity is limited by T cell receptor (TCR) but in vitro expansion is easily achievable. We show that from buffy coats of healthy donors isolated and CRISPR/Cas9-mediated BCL11B knock-out CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics and combine spontaneous and antibody-dependent NK cell cytotoxicity with T cell capability for rapid in vitro expansion. The observed features of the induced innate CD8+ (iiT8) cells make them an interesting and promising tool for cellular therapy.

2022-12-07 | E-MTAB-12064 | biostudies-arrayexpress

scRNAseq of immune cells of patients with chronic graft-versus-host disease

Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.

2024-04-10 | E-MTAB-13419 | 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 sequencing of lung carcinoma

Project description:Single cell sequencing of 5 dissected lung tumors.

2018-07-09 | E-MTAB-6149 | biostudies-arrayexpress