README.md

Nanobody-tethered transposition followed by sequencing (NTT-seq)

This repository contains code needed to reproduce the analyses shown in Stuart et al. (2022), Nature Biotechnology

More information about NTT-seq can be found at the NTT-seq website

Installing dependencies

All the required dependencies needed to run the workflow can be installed automatically by creating a new conda environment.

First ensure that conda or mamba is installed and available.

To create a new environment with the dependencies installed, run:

# using conda
conda env create -f environment.yaml

# using mamba
mamba env create -f environment.yaml

Running the workflow

This workflow involves downloading data from AWS using the AWS command line tools. To enable the download, you will first need to create an AWS account and set up the AWS command line tools by running aws configure. Note that some of the data downloaded may incur charges from AWS.

To run the Snakemake workflow, first activate the conda environment containing the required dependencies:

conda activate ntt

Next, run snakemake with the desired options. Setting the -j parameter controls the maximum number of cores used by the workflow:

snakemake -j 24

See the snakemake documentation for a complete list of available options.

Data availability

Processed datasets from this study are available from:

• GEO: GSE212588
• SRA: SRP395379
• Zenodo: 7102159
• dbGaP: phs003068.v1.p1

Plasmid availability

Plasmids generated from this study are available from AddGene:

• pTXB1-nbOcIgG-Tn5
• pTXB1-nbMmKappa-Tn5
• pTBX1-nbMmIgG1-Tn5
• pTBX1-nbMmIgG2a-Tn5

Citation

@ARTICLE{Stuart2022,
  title    = "Nanobody-tethered transposition enables multifactorial chromatin
              profiling at single-cell resolution",
  author   = "Stuart, Tim and Hao, Stephanie and Zhang, Bingjie and
              Mekerishvili, Levan and Landau, Dan A and Maniatis, Silas and
              Satija, Rahul and Raimondi, Ivan",
  journal  = "Nat. Biotechnol.",
  month    =  dec,
  year     =  2022,
  url      = "http://dx.doi.org/10.1038/s41587-022-01588-5",
  language = "en"
}