Dataset Information

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.

ABSTRACT: Mouse heart development arises from Mesp1-expressing cardiovascular progenitors (CPs) that are specified during gastrulation. The molecular processes that control early regional and lineage segregation of CPs have been unclear. We performed single-cell RNA sequencing of wild-type and Mesp1-null CPs in mice. We showed that populations of Mesp1 CPs are molecularly distinct and span the continuum between epiblast and later mesodermal cells, including hematopoietic progenitors. Single-cell transcriptome analysis of Mesp1-deficient CPs showed that Mesp1 is required for the exit from the pluripotent state and the induction of the cardiovascular gene expression program. We identified distinct populations of Mesp1 CPs that correspond to progenitors committed to different cell lineages and regions of the heart, identifying the molecular features associated with early lineage restriction and regional segregation of the heart at the early stage of mouse gastrulation.

SUBMITTER: Lescroart F

PROVIDER: S-EPMC6556615 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.

Lescroart Fabienne F Wang Xiaonan X Lin Xionghui X Swedlund Benjamin B Gargouri Souhir S Sànchez-Dànes Adriana A Moignard Victoria V Dubois Christine C Paulissen Catherine C Kinston Sarah S Göttgens Berthold B Blanpain Cédric C

Science (New York, N.Y.) 20180125 6380

Mouse heart development arises from Mesp1-expressing cardiovascular progenitors (CPs) that are specified during gastrulation. The molecular processes that control early regional and lineage segregation of CPs have been unclear. We performed single-cell RNA sequencing of wild-type and Mesp1-null CPs in mice. We showed that populations of Mesp1 CPs are molecularly distinct and span the continuum between epiblast and later mesodermal cells, including hematopoietic progenitors. ...[more]

PMID: 29371425

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Project description:Mouse heart development arises fromMesp1 expressing cardiovascular progenitors that are specified at the early stage of gastrulation. Lineage tracing and clonal analysisof Mesp1 progenitors revealed that heart development arises from distinct populations of Mesp1+ cardiovascular progenitors (CPs) expressing Mesp1 at different time points during gastrulation that contribute to different heart regions and different cardiovascular lineages. However, it remains unclear what are the molecular mechanisms that control the early regional and lineage segregation of Mesp1 CPs. Here, we performedsingle cell RNA-sequencing of FACS isolated Mesp1 CPs in WT and Mesp1 null embryos at different times to define the cellular and molecular heterogeneity of the Mesp1CPs, identify the role of Mesp1 in regulating cellular heterogeneity and uncover the mechanisms associated with lineage and regional segregation during the early stages of gastrulation.We showed that Mesp1 CPs isolated at E6.75 and E7.25 are molecularly distinct and make the continuum betweenepiblast and later mesodermal cells including hematopoietic progenitors. Single cell transcriptome of Mesp1 deficient CPsshowed that Mesp1 is required for the exitof thepluripotent state and the induction of the cardiovascular gene expression program in vivo.Using dimensional reduction analysis, we identified distinct populations of Mesp1 CPs that correspond to progenitors committed to different celllineages and regions of the heart, identifying the molecular features associated with the early lineage and regional segregation. Notch1CREER lineage tracing, a marker preferentially expressed by one of the different Mesp1CP subpopulations, during the early stage of gastrulation marked almost exclusively ECs, demonstrating theexistence of an early Mesp1 subpopulation committed to the EC fate.This study uncoversthe cellular and molecular heterogeneity associated with early lineage restriction and regional segregation of the heart at the early stage of gastrulation.

Project description:We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (CSC) and differentiated (FCS) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers. Operative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples). SMART-seq protocol was implemented to generate single cell full length transcriptomes (modified from Shalek, et al Nature 2013) and sequenced using 25 bp paired end reads. Single cell cDNA libraries for MGH30 were resequenced using 100 bp paired end reads to allow for isoform and splice junction reconstruction (96 samples, annotated MGH30L). Cells were also cultured in serum free conditions to generate gliomasphere cell lines for MGH26, MGH28, and MGH31 (CSC) which were then differentiated using 10% serum (FCS). Population RNA-seq was performed on these samples (3 CSC, 3 FCS, 6 total). The initial dataset included 875 RNA-seq libraries (576 single glioblastoma cells, 96 resequenced MGH30L, 192 single gliomasphere cells, 5 tumor population controls, 6 population libraries from CSC and FCS samples). Data was processed as described below using RSEM for quantification of gene expression. 5,948 genes with the highest composite expression either across all single cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. The final processed dataset then included 430 primary single cell glioblastoma transcriptomes, 102 single cell transcriptomes from cell lines(GBM6,GBM8), 5 population controls (1 for each tumor), and 6 population libraries from cell lines derived from the tumors (CSC and FCS for MGH26, MGH28 and MGH31). The final matrix (GBM_data_matrix.txt) therefore contains 5948 rows (genes) quantified in 543 samples (columns). Please note that the samples which are not included in the data processing are indicated in the sample description field.

Dataset Information

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.

Publications

Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq.

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