Integrated elastomeric valves, also referred to as Quake valves, enable precise control and manipulation of fluid within microfluidic devices. Fabrication of such valves requires bonding of multiple layers of the silicone polymer polydimethylsiloxane (PDMS). The conventional method for PDMS-PDMS bonding is to use varied ratios of base to crosslinking agent between layers, typically 20:1 and 5:1. This bonding technique, known as 'off-ratio bonding', provides strong, effective PDMS-PDMS bonding for multi-layer soft-lithography, but it can yield adverse PDMS material properties and can be wasteful of PDMS. Here we demonstrate the effectiveness of 'on-ratio' PDMS bonding, in which both layers use a 10:1 base-tocrosslinker ratio, for multilayer soft lithography. We show the efficacy of this technique among common variants of PDMS: Sylgard 184, RTV 615, and Sylgard 182.

Highlights d New microfluidic device images and sorts single cells then performs single-cell DamID d Improved m6 A-Tracer method images protein-DNA interactions with less background d mDamID identifies LADs that vary between single cells and across cell types d Imaging can be used to select cells with greater DamID sequencing signal to noise

Integrated elastomeric valves, also referred to as Quake valves, enable precise control and manipulation of fluid within microfluidic devices. Fabrication of such valves requires bonding of multiple layers of the silicone polymer polydimethylsiloxane (PDMS). The conventional method for PDMS-PDMS bonding is to use varied base to crosslinking agent ratios between layers, typically 20:1 and 5:1. This bonding technique, known as "off-ratio bonding," provides strong, effective PDMS-PDMS bonding for multi-layer soft-lithography, but it can yield adverse PDMS material properties and can be wasteful of PDMS. Here we demonstrate the effectiveness of onratio PDMS bonding for multilayer soft lithography. We show the efficacy of this technique among common variants of PDMS: Sylgard 184, RTV 615, and Sylgard 182.

1 2 Genome regulation depends on carefully programmed protein-DNA interactions that maintain or 3 alter gene expression states, often by influencing chromatin organization. Most studies of these 4 interactions to date have relied on bulk methods, which in many systems cannot capture the 5 dynamic single-cell nature of these interactions as they modulate cell states. One method allowing 6 for sensitive single-cell mapping of protein-DNA interactions is DNA adenine methyltransferase 7 identification (DamID), which records a protein's DNA-binding history by methylating adenine 8 bases in its vicinity, then selectively amplifies and sequences these methylated regions. These 9interaction sites can also be visualized using fluorescent proteins that bind to methyladenines. Here 10 we combine these imaging and sequencing technologies in an integrated microfluidic platform 11 (µDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We apply 12 this system to generate paired single-cell imaging and sequencing data from a human cell line, in 13 which we map and validate interactions between DNA and nuclear lamina proteins, providing a 14 measure of 3D chromatin organization and broad gene regulation patterns. µDamID provides the 15 unique ability to compare paired imaging and sequencing data for each cell and between cells, 16 enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-17