If you’re interested in trying MULTI-ATAC yourself, have a look at the protocol in the SI, and reach out to me for further details about oligos and barcode sequences.

MULTI-ATAC has already been successfully applied in other contexts as well. In this work, my collaborator Katya used MULTI-ATAC to probe the mechanisms by which deleterious mutations accumulate in the mitochondrial genome during aging:
www.biorxiv.org/content/10.1...

By including multiple replicates and doses per drug, we discover high-confidence drug-responsive chromatin regions and genes. We show that EZH2 degradation via MS177 coincides with up-regulation of NF-kB signaling, and SWI/SNF perturbation elicits a potent type I interferon response.

MULTI-ATAC is also compatible with the 10x Genomics Multiome kit. To demonstrate the type of high-throughput experiment enabled by MULTI-ATAC, we perform a 96-plex multiomic drug assay comparing inhibition and degradation of different epigenetic remodelers in a model of primary immune activation.

To combat this, we re-designed our MULTI-seq method and optimized it to enable pooled transposition of barcoded nuclei on the 10x Genomics scATAC-seq platform. We show that pooled transposition with MULTI-ATAC completely negates the batch effects that arise from processing samples separately.

The effect of variable transposition is well-established in bulk ATAC data but surprisingly has not to our knowledge been examined in scATAC-seq. This is especially important to consider when unique samples (i.e., different patients, disease states, etc.) are transposed in a parallel format.

For example, we see that variability in Tn5:nuclei ratios unsurprisingly skews per-nucleus fragment yields. However, this impacts dimensionality reduction and - importantly - even biases cell type recovery.

scATAC-seq data across different technologies and sample types suffer from batch effects that are linked to transposition reaction conditions and directly impact biological interpretation.

Happy to share that the preprint to our new scATAC-seq multiplexing method, MULTI-ATAC, is officially online:
www.biorxiv.org/content/10.1...