Release Updates

  • 06/09/2019 adds summitmatrix.sparse.binary.rds, tsnecoords.txt.gz, and densitypeakclusters.txt.gz files for all three timepoints.
  • 03/14/2018: Initial release.

Tutorial Data

Here are links to all of the data used in the tutorial (code is presented for downloading and processing these files through the course of the tutorial too).

Name Last modified Size Description
irlba_1.0.3.tar.gz 18-Nov-2017 17:20 177K Source code for irlba version 1.0.3, the version used for latent semantic indexing in Cusanovich, Reddington, Garfield et al.
monocle_2.3.5.tar.gz 18-Nov-2017 17:20 16M Source code for Monocle version 2.3.5, the version used for pseudotemporal ordering in Cusanovich, Reddington, Garfield et al.
DDRTree_0.1.4.tar.gz 16-Jan-2018 11:23 12K Source code for DDRTree version 0.1.4, the version used for pseudotemporal ordering in Cusanovich, Reddington, Garfield et al.
monocle_patch.R 18-Nov-2017 17:20 6.6K A small update to Monocle that causes the differentialGeneTest to return beta values.
6to8.2kbmatrix.sparse.binary.rds 18-Nov-2017 17:20 113M A binary matrix recording whether insertions were observed in 2kb windows throughout the genome in all 6-8 hour cells. This file is provided as a sparse matrix in .rds format so that it can be easily loaded into R.
6to8.summitmatrix.sparse.binary.rds 18-Nov-2017 17:19 69M A binary matrix recording whether insertions were observed in a master list of potential regulatory elements in all 6-8 hour cells. This file is provided as a sparse matrix in .rds format so that it can be easily loaded into R.
6to8.xycalls.txt 18-Nov-2017 17:19 300K A file assigning a sex to each cell from the 6-8 hour time point on the basis of reads mapping to the sex chromosomes. A 1 indicates male and a 2 indicates female.
6to8.read.report.txt 18-Nov-2017 17:19 429K A file reporting the total number of unique reads recovered from each cell. This was used in the logistic regression analysis to control for cells having varying complexity.
2to4_files.tar.gz 18-Nov-2017 17:19 44M A tarball of all the files required for pseudotemporal ordering of cells from the 2-4 hour time point.

Accessibility Matrices

Here we make peak of accessibility by cell matrices for all three time points. Each matrix is a sparse matrix file in .rds format. Requires the Matrix package in R to open.

Name Last modified Size Description
2to4.summitmatrix.sparse.binary.rds 8-Jun-2019 07:05 59M Accessiblity matrix for the 2-4hr timepoint.
6to8.summitmatrix.sparse.binary.rds 18-Nov-2017 17:19 69M Accessiblity matrix for the 6-8hr timepoint. The same file is also available in the Tutorial section and is just reproduced here for consistency.
10to12.summitmatrix.sparse.binary.rds 9-Jun-2019 14:37 48M Accessiblity matrix for the 10-12hr timepoint.

t-SNE Coordinates

Here we make t-SNE coordinates for each timepoint available. See the manuscript for how t-SNE coordinates were calculated. Each file is a gzipped .tsv and includes 3 columns: Cell ID column, x-axis coordinate column, y-axis coordinate column.

Name Last modified Size Description
2to4.tsnecoords.txt.gz 9-Jun-2019 15:12 165K t-SNE coordinates for the 2-4hr timepoint.
6to8.tsnecoords.txt.gz 9-Jun-2019 15:12 162K t-SNE coordinates for the 6-8hr timepoint.
10to12.tsnecoords.txt.gz 9-Jun-2019 15:12 149K t-SNE coordinates for the 10-12hr timepoint.

Cluster Assignments

Here we make the density peak-based cluster assignments (derived from the t-SNE coordinates) for each timepoint available. See the manuscript for how t-SNE coordinates were calculated and how density peak clusters were identified. Each file is a gzipped .tsv and includes 2 columns: Cell ID column, cluster assignment.

Name Last modified Size Description
2to4.densitypeakclusters.txt.gz 8-Jun-2019 05:42 34K Cluster assignments for the 2-4hr timepoint.
6to8.densitypeakclusters.txt.gz 8-Jun-2019 05:42 34K Cluster assignments for the 6-8hr timepoint.
10to12.densitypeakclusters.txt.gz 8-Jun-2019 05:41 31K Cluster assignments for the 10-12hr timepoint.