Improve Research Reproducibility A Bio-protocol resource
bpdetail_icon_lock
Preprint

Cell cycle prediction

AK Anneke Dixie Kakebeen
AW Andrea Elizabeth Wills

Last updated date: Oct 29, 2020 Views: 980 Forks: 0

original An abbreviated version of this protocol was published in eLife in Apr, 2020
Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
download pdf Download PDF
ask Ask a question
cite How to cite
nfavorite Favorite

Cell cycle prediction analysis was performed using the Seurat software in R. 


We referenced this vignette to do our analysis:

https://satijalab.org/seurat/v3.1/cell_cycle_vignette.html

Under the heading: "Assign Cell-cycle Scores"



Reference to the code used to perform analysis and make figures was uploaded to gitlab and has been provided in our paper. The only modifcation made to the above vignette was removing genes in Seurat's cell cycle modules that we did not have in our dataset and using the remaining genes to run the command "CellCycleScoring":

https://gitlab.com/akakebee/kakebeen-et-al-2020/-/blob/master/SingleCell_1/UMAP/SCRNA_Seurat_UMAP_1.Rmd

Under the heading: "## Cell cycle analysis”


Copyright: Content may be subjected to copyright.
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Kakebeen, A and Wills, A(2020). Cell cycle prediction. Bio-protocol Preprint. bio-protocol.org/prep585.
  2. Kakebeen, A. D., Chitsazan, A. D., Williams, M. C., Saunders, L. M. and Wills, A. E.(2020). Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors. eLife. DOI: 10.7554/eLife.52648

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A
This protocol preprint was submitted via the "Request a Protocol" track.