10.5281/zenodo.4597857
https://zenodo.org/records/4597857
oai:zenodo.org:4597857
Tekman, Mehmet
Mehmet
Tekman
0000-0002-4181-2676
University of Freiburg
Galaxy Training Material for single-cell RNA-seq tutorial with Plant Datasets
Zenodo
2021
galaxy
training
scRNA
scRNA-seq
single-cell
2021-03-11
eng
Interactive resource
10.5281/zenodo.4597856
https://zenodo.org/communities/galaxy-training
0.1
Creative Commons Attribution 4.0 International
These are the raw expression matrices from Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing (Denyer et al., 2019). In the paper they were processed using Seurat under a tSNE embedding, and in this tutorial we will replicate the analysis using ScanPy under a UMAP embedding.
The initial datasets used generic Uniprot identifiers and required transposing. The method required to pull, annotate, unambiguously exchange names, and transpose these datasets to help with analysis are contained within the uniprot.R script included (with the remapping.complete.tsv.gz being generated by this).
Original datasets from GSE123818:
GSE123818_Root_single_cell_shr_datamatrix.csv
GSE123818_Root_single_cell_wt_datamatrix.csv
Updated using the scripts (for the GTN):
GSE123818_Root_single_cell_shr_datamatrix.fixednames.transposed.csv.gz
GSE123818_Root_single_cell_wt_datamatrix.fixednames.transposed.csv.gz