Reproducibility

Reproducing and extending our works

Our team is an advocate for open and reproducible science. This includes both experimental details to generate data and line-by-line computational workflows to reproduce critical insights. As many of our own insights come from reanalyzing data from previously published work, we take special care to ensure that resources from our works are available in easy-to-access formats.

Check out our curated resources from our major efforts here:

Lareau Lab @ MSKCC (2024-)

Programmable Enrichment via RNA FlowFISH by sequencing

PERFF-seq is new workflow for studying rare cell types via nucleic acid cytometry upstream of scRNA-seq. Our resources highlight code to reproduce downstream analyses of PERFF-seq data as well as step-by-step protocols for performing your own experiment.

PERFF-seq · 13 Oct 2024 · Led by Tsion with Satpathy Lab and SAIL

Code

Datasets

Protocol

Before MSKCC (2019-2023)

2023

Viral reactivation uncovered in existing genomics datasets

These resources provide an overview for mining existing human sequencing datasets for the presence of viral nucleic acids. We used this framework to discover the reactivation of HHV-6 during T cell culture, including in the manufacturing of therapeutic CAR T cells. Code and data for this work are outlined here.

Viruses in -seq data · 30 Nov 2023 · with the Satpathy Lab

Downstream analyses

Datasets

Human pan-viral screen

Mitochondrial single-cell ATAC-seq

The best established method for generating high-quality insights of clonal relatedness using single-cell genomics is the mtscATAC-seq protocol. Check out our code, datasets, and step-by-step protocols here.

mtscATAC-seq · 15 Feb 2023 · with Leif via the Sankaran Lab

2022

Mitochondrial Alteration Enrichment from Single-cell Transcriptomes to Establish Relatedness

A parisomonious method common for profiling 3' scRNA-seq with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling clonal tracing.

MAESTER · 24 Feb 2022 · with Ty Miller Lab and Peter van Galen Lab

2021

Combined proteomic and epigenomic profiling via M13 Bacteriophages

PHAGE-ATAC allows for a multi-omic extension of the scATAC-seq workflow by using M13 bacteriophages displaying nanobodies to quantify proteo-genomic measurements. Code, data, and plasmids to get started are available here.

PHAGE-ATAC · 30 Oct 2021 · with Evenij Fiskin in the Regev Lab</a>

Datasets

Downstream analyses

Phage plasmid

ATAC with Selected Antigen Profiling via sequencing + DOGMA-seq

ASAP-seq and DOGMA-seq extend commercial kits from 10x Genomics for multi-omic measurements of intracellular and surface proteins alongside accessible chromatin (and the transcriptome). These resources enable an end-to-end experimental workflows and computational analyses.

ASAP-seq/DOGMA-seq · 06 Jun 2021 · with Eleni Mimitou and Peter Smibert</a>

2020

Uncovering barcode multiplets in 10x scATAC-seq data

Barcode multiplets occur when either a bead contains multiple valid cell barcodes or when multiple beads becomes encapsulated inside a single droplet. We outline tools and results that can detect barcode multiplets in sequencing dataset and quantify their impact.

Barcode multiplets · 13 Feb 2020 · with the Buenrostro Lab

Processing pipeline

Datasets

Downstream analyses

2019

Droplet-based single-cell ATAC-seq

The dscATAC-seq method is a highly scalable droplet-based workflow for the Assay for Transposase Accessible Chromatin via sequencing developed by experimental and computational insights. This approach is now commercially available.

dscATAC-seq · 20 Aug 2019 · with Fabina and Jen via the Buenrostro Lab