Dataset for "Protein velocity and acceleration from single-cell multiomics experiments." Source data from 10X Genomics at https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_protein_v3 and https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_protein_v3.

Protein count data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685243, file GSM2685243_protein_2_PBMCs_matrix.txt.gz, and processed into csv format. Aligned bam file was acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2685238, file mRNA_2_PBMCs_possorted_genome_bam.bam. velocyto processing: ve...

Protein data were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3596101, file GSM3596101_CTCL-ADT-count.csv.gz. velocyto processing: velocyto run (bam directory)/(BAM file).bam (transcriptome directory)/genes/genes.gtf

Protein counts were acquired from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866. LOOM was generated from FASTQ. cellranger processing: cellranger count --id=(desired bam directory) --transcriptome=(transcriptome directory) --fastqs=(fastq directory) --localcores=40 --localmem=100 --chemistry=SC3Pv2 velocyto processing: velocyt...

VR environment with a 3D model of a Nucleosome consisting of Histones and DNA (Based on crystal structure 5JRG). You can generate new instances of the protein by clicking the controller trigger grip. Hold the trigger down to look at the structure and release to drop. The structure was rendered in VMD and built with Unity 5.6 for use with Stea...

Raw data and simulation code for manuscript "A synthetic protein-level neural network in mammalian cells"

mitochondrial Unfolded Protein Response ATFS-1 targets

Overview This repository contains code and data for analysis and plotting related to the development of synthetic RNA export systems and their application for non-destructive measurement of cell dynamics and delivering RNA from cell to cell. Citation If you use this code, please cite this paper. Horns et al., Engineering RNA export for measureme...

The system and trajectory of the relaxation of a structural model of Sgt2-C by all-atom molecular dynamics. In the accompanying paper, Sgt2-C is inferred to be a STI1 domain. Further details about the simulation protocols and results can be found within the accompanying paper and repository.

This folder provides all data and code needed to reproduce the analysis and figures of Chapter 2 ("Ligand-Receptor Promiscuity Enables Complex Computations") in the associated thesis, "Principles of Addressing Specificity in Promiscuous Ligand-Receptor Systems." All code is written in Python, with analysis provided in a Jupyter notebook.