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High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer (Pierce SE*, Granja JM*, et al. 2020)

Link : https://www.biorxiv.org/content/10.1101/2020.11.02.364265v1

Please cite : Pierce SE et al., High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer. bioRxiv (2020)

Download Information

Installation Time (10-20 seconds)

Align Barcodes Run Time (10-20 minutes)

Spear ATAC Analysis (~30 min - 2 hours - depending on data size)

Dependencies are as listed in the individual files but here are the overall versions used

R 3.6.1 - ArchR, ShortRead, readr, data.table, fastmatch, magrittr
Python 3.6.1 - snakemake

sgRNA Align Barcodes (See AlignSgRNA Folder)

Scripts (See Scripts Folder)

RunSnakemake.sh - Bash executable to run snakemake analysis (bash RunSnakemake.sh)

Snake-Align-sgRNA.py - Snakemake for sgRNA Align Analysis.

SpearATAC-Align-sgRNA.R - Code for analysis of SpearATAC Screen.

Data Files (See data Folder)

10x-Barcodes.txt - 10x Genomics Cell Barcodes for scATAC-seq

K562_Large_1_I2-Downsampled.barcoded.fastq.gz - Amplified SpearATAC cell barcodes.
K562_Large_1_R1-Downsampled.barcoded.fastq.gz - Amplified SpearATC sgRNA barcodes.

sgRNA-K562-Pilot.txt - sgRNA barcodes for K562 Pilot screen (change in Snake-Align-sgRNA.py)
sgRNA-K562-TimeCourse.txt - sgRNA barcodes for K562 Time Coures screen (change in Snake-Align-sgRNA.py)
sgRNA-LargeScreen.txt - sgRNA barcodes for Large screens (change in Snake-Align-sgRNA.py)

Analysis of scATAC + sgRNA data (See AnalyzeSpearATAC Folder)

Scripts (See Scripts Folder)

Download-Test-SpearATAC-Data.R - Code for downloading SpearATAC test data.

Analysis-of-Spear-ATAC-Screen.R - Code for analysis of SpearATAC Screen.

SpearATAC-Functions.R - Helper Functions for SpearATAC Analysis.

Data Files (See data Folder)

K562_R1.fragments.tsv.gz - 10x Genomics Fragment Files
K562_R2.fragments.tsv.gz - 10x Genomics Fragment Files

K562_R1.singlecell.csv - 10x Genomics Summary Stats containing cells passing filters
K562_R1.singlecell.csv - 10x Genomics Summary Stats containing cells passing filters

K562_R1.sgRNA.rds - SpearATAC sgRNA Files containing Barcode Alignments
K562_R2.sgRNA.rds - SpearATAC sgRNA Files containing Barcode Alignments

Vierstra-Human-Motifs.rds - Motifs from Vierstra et al Nature 2020