Fig. 2: Micropatterning hydrogel porosity to enable selective nucleic acid extraction.

a Cells encapsulated in a porous hydrogel. b Micropatterning a 50 µm void in the non-porous hydrogel using a 10× objective. c Further micropatterning a 12 µm void using a 20× objective. d Bright-field micrographs of a 50 µm disk of porous hydrogel surrounded by non-porous hydrogel. e Diffusion of FITC-Dextran (Mw 10 kDa) into the porous hydrogel disk. g, h Selective single cell lysis using UM-UC13-mCherry (mCh) and UM-UC13-EGFP (EGFP) cells shown using overlaid bright-field and fluorescence micrographs. f mCh and EGFP cells encapsulated in porous hydrogel. g All non-target cells are embedded in non-porous hydrogel, while exposing a single target EGFP cell. h After addition of cell lysis buffer, only the target EGFP cell was lysed. Fluorescence of non-target cells is reduced due to dehydration, but not eliminated. i qPCR for RNA selectively extracted from mixed mCh and EGFP cell samples including no-template control (NT), bulk mCh, bulk EGFP, single cell mCh, single cell EGFP, as well as one mCh and one EGFP cell. Black arrows indicate target cDNA undetectable. Ct values are averaged from N = 5. j See-N-Seq analysis from mixtures of mouse and human cells. The scatter plot shows the number of unique human and mouse transcripts associating to each sample. Blue dots indicating mouse single cells while red dots indicating human single cells. N = 5. k Mapped UMI counts per each sample group. All scale bars = 50 µm.