Single-nucleus ATAC-seq of E8.25 mouse embryos
This is the website accompanying the manuscript Pijuan-Sala, B., et al., Nat. Cell Biol., 2020. A custom UCSC Genome Browser session is available here.
This website contains the following tabs:
Experimental design: Here, you can find a brief outline of the experimental design of this dataset.
Topics: Here, you can explore the contribution of each topic to each nucleus and the transcription factor enrichment results for each topic.
Single-cell TF enrichment: Here, you can visualise the enrichment scores for transcription factors at the single-cell level, computed using chromVAR (Schep et al., Nature Methods, 2017) .
Genomic regions: Here, you can browse the list of genomic regions and their associated details.
Accessibility of OCRs: Here, you can check the accessibility for specific genomic coordinates in the UMAP visualisaiton.
Allantoic-haemato-endothelial landscape: Here, you can check the accessibility for specific genomic coordinates in the UMAP visualisaiton for the allantoic-haemato-endothelial subset.
Dynamic patterns towards endothelium: Here, you will visualise the dynamic patterns of accessibility and access transcription factor enrichment results.
External links: Here, we provide links to the paper, the data and the code used for the analysis.
We dissected mouse embryos at days 8.25 post-fertilisation and snap-froze them. Samples were then processed using single-nucleus ATAC-seq with slight modifications (please see the publication for further details).
TF enrichment analysis on regions uniquely contributing to the topic
Check the regions contributing to each topic in the Genomic regions tab!
You can browse the list of genomic coordinates below. By pressing the download button, you will be able to export your desired list of coordinates with their details into a .csv file. Please note that if a genomic region is assigned to multiple genes, the entry for this region will be repeated as many times as the number of associated genes.
The plot below shows the percentage of nuclei with the genomic region accessible per cell type. On top of the bars, you will find the actual number of nuclei with accessibility at the specified locus.
The plot below shows the percentage of nuclei with the genomic region accessible per cell type. On top of the bars, you will find the actual number of nuclei with accessibility at the specified locus.
Paper: This analysis is part of: Pijuan-Sala, B., et al., Nat. Cell Biol., 2020
Data: Data has been deposited at GEO: GSE133244. Raw fastq files with their barcodes can also be downloaded here.
UCSC session: Explore the Bigwig tracks for each cell type in our UCSC session.
Code: Code used to analyse this dataset is available at https://github.com/BPijuanSala/MouseOrganogenesis_snATACseq_2020. It contains a README.md file explaining each step of the code.
Citing this website: If you use this website, we would be grateful if you could cite: Pijuan-Sala, B., et al., Nat. Cell Biol., 2020