Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

Here we provide the entire processing pipeline for reproducing the results in the manuscript (see our BioRxiv preprint, now published in BMC Biology). This pipeline may facilitate the study of transposable elements (TEs) in the context of stem cell development and other cell type transition systems. We also provide a web interface at https://bis.zju.edu.cn/hscTE to visualize TE and gene expression during human and mouse EHT. The multi-faceted display (including TEs, CpG, cCREs, peaks and genome coverages) of mouse EHT scATAC-seq data is available from https://bis.zju.edu.cn/hscTE/jbrowse/?data=mouse.

Execution requirements

• R (recommend >=4.2)
• Python (recommend >=3.9)
• Jupyter Notebook (Optional but recommend)
• Other packages (see session info at the end of each notebook)

Pipelines and data

• TE landscape analysis

1. TE_landscape (Fig. 1): Jupyter | Source data

• Human data processing

1. EHT_RNA_Preprocessing (Fig. 2): Jupyter | Source data
2. EHT_Trajectory_Reconstruction (Fig. 2, Fig. 8): Jupyter | Source data
3. EHT_TE_Expression (Fig. 2, Fig. 3, Fig. 4, Fig. 8): Jupyter 1, Jupyter 2 | Source data
4. EHT_TE_hdWGCNA (Fig. 3): Jupyter | Source data
5. EHT_TE_Silencing_Relaxation (Fig. 4): Jupyter | Source data
6. EHT_TE_Sensing (Fig. 5): Jupyter | Source data
7. EHT_Spatial_Transcriptome (Fig. 8): Jupyter | Source data
8. EHT_TE_Hypoxia (Fig. 8): Jupyter | Source data
9. HUVEC_Hypoxia_Bulk (Fig. 8): Jupyter | Source data

• Mouse data processing

1. EHT_RNA_Preprocessing (Fig. 2): Jupyter | Source data
2. EHT_Trajectory_Reconstruction (Fig. 2): Jupyter | Source data
3. EHT_TE_Expression (Fig. 2, Fig. 3, Fig. 4): Jupyter | Source data
4. EHT_TE_hdWGCNA (Fig. 3): Jupyter | Source data
5. EHT_TE_Silencing_Relaxation (Fig. 4): Jupyter | Source data
6. EHT_TE_Sensing (Fig. 5): Jupyter | Source data
7. EHT_TE_ATAC (Fig. 6, Fig. 7): Jupyter 1, Jupyter 2, Jupyter 3 | Source data

• Human and mouse data integration

1. Integration (Additional file 5): Jupyter | Source data

Cite

Feng, C., Tie, R., Xin, S. et al. Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition. BMC Biol 22, 143 (2024).