Seq-Well: A portable, low-cost platform for single-cell RNA-seq of low-input samples

Single-cell RNA -seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA -seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We characterize Seq-Well extensively and use it to profile thousands of primary human macrophages exposed to tuberculosis. Overall design: Single-cell RNA sequencing experiments of HEK/3T3 mixing, PBMCs, and TB-exposed Macrophages.