Embryonic Mammalian Heart Development
RNAseq Atlas of Mesp1 Progenitors During Mammalian Heart Development
Introduction
Mesp1 marks the most primitive multipotent cardiac progenitors for mammalian heart develoment. In this study, single cell unbiased whole transcriptome RNAseq analysis was performed in mouse embryos Mesp1-GFP+ cells at 2 time points: E6.75 and E7.25. In addition, the E6.75 cells consist of two conditions: Knock-out (KO) and wild-type (WT).
In total Batch 1 has 341 cells passed quality control (QC), among which 168 are E6.75 cells (83 WT and 85 KO) and 173 are E7.25 cells. Batch 2 has 257 cells passed QC, including 89 E6.75 WT cells and 168 E7.5 WT cells.
In addition, there are 294 cells (turquoise/E6.5 epiblast Mesp1+ cells and blue/E7.5 Mesp1+/Flk1+ cells) selected from the nature paper. It can be observed that the E6.75 and E7.25 Mesp1+ cells are well spanning the gap between the E6.5 and E7.5 cells.
Data
Download matrix of gene counts here. Metadata is available here.
The gene counts are raw counts generated from HTSeq-count. In total, there are 892 cells, including 598 new generated cells from two batches and 294 cells from our previous study which can be played around with here Scialdone2016.
The metadata is consisted of 11 columns:
- ID: Cell names that match the names of GEO submission
- Type: WT -> Wild Type; KO -> Knock Out
- Stage: Embryonic days: E6.5 (Epiblast)/E6.75/E7.25/E7.5
- Study: B1 (Batch1); B2 (Batch2); WJ (Scialdone2016 data)
- Condition: Stage + Type
- Species: Mouse
- DCT: Destination cells assigned (DCT1-5 and Starting cells)
- SPRING_Co_WJpWTpKO: SPRING coordinates of WJ+WT+KO
- SPRING_Co_WJpWT: SPRING coordinates of WJ+WT
- SPRING_Co_WT: SPRING coordinates of WT only
- DE_ct12: Cells used for Differential expression analysis between DCT1 and DCT2
The raw counts were normalised using the R package Scran, batch corrected by Combat in sva R package and highly variable genes were identified using the method of Brennecke et al. (2013). The resulting expression matrix that was used to generate the following SPRING plot can be found here.
Entire dataset (SPRING)
Click on an image to activate interactive plot.
