Anneke Kakebeen 13 Aug 2019
- Repository for analysis of data from Kakebeen et al 2020
- Abstract
- ATAC
- SingleCell_1
- GRN
- Tail Measurement
- Regen PH3
This GitLab project holds code for sequencing data preparation, analysis, and figure making for the publication titled Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors. eLife 2020;9:e52648 DOI: 10.7554/eLife.52648.
Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.
This folder contains the commands used to take raw reads to a counts table, quality control analysis, differential accessiblity analysis, and the figures made from this data.
This folder contains the Seurat integrative clustering analysis used to cluster the data, differential expression analysis, and code for figures made from this data.
This folder contains the code used to integrated the ATAC-Seq, scRNA-Seq, and Change et al Bulk RNA-Seq for grn prediction and analaysis.
This folder contains the tail measurement data and graphical representations of this data for vivo-morphants and embryonic morphants.
This folder contains data and visuali representations of the number of PH3 + cells per reenerated area of the spinal cord in normal regeneration as well as morphant regeneration.