Lesson Open Access

Galaxy Training Material for single-cell RNA-seq tutorial with Plant Datasets

Tekman, Mehmet

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

 

Files (69.1 MB)
Name Size
gene.annotations.csv
md5:32da56838e2998262356d166afa2e49e
548.0 kB Download
GSE123818_Root_single_cell_shr_datamatrix.csv.gz
md5:ea67516dbf6424b66457d3f360088ca0
4.9 MB Download
GSE123818_Root_single_cell_shr_datamatrix.fixednames.transposed.csv.gz
md5:e1347c1accb21cf16d12e20f23344b56
5.6 MB Download
GSE123818_Root_single_cell_wt_datamatrix.csv.gz
md5:96af50339415691a42514800d923ec54
25.4 MB Download
GSE123818_Root_single_cell_wt_datamatrix.fixednames.transposed.csv.gz
md5:8fd09cf2b836f3bbd10e20ac9c9a3053
32.3 MB Download
remapping.complete.tsv.gz
md5:7c412d7e16fed504cfc35ca358858758
349.1 kB Download
uniprot.R
md5:19d97f7478cecb0ee6ce42db77fcb0c0
3.3 kB Download
21
58
views
downloads
All versions This version
Views 2121
Downloads 5858
Data volume 723.6 MB723.6 MB
Unique views 2121
Unique downloads 4141

Share

Cite as