Disclosed herein include methods of specifying sites (e.g., sites for colony formation) on a surface (e.g., a planar surface) and generating a flow cell having the sites specified on a surface. Also disclosed are methods of performing sequencing (e.g., sequencing-by-synthesis and sequencing-by-binding) using the flow cell generated and processing (e.g., aligning, orienting, sorting, and assessing quality) images of the flow cell captured during sequencing.

A method of manufacturing a patterned substrate for culturing cells. The method includes the steps of: (1) preparing a substrate, (2) forming a first plasma polymer layer by integrating a first precursor material on the substrate using a plasma, wherein the first plasma layer inhibits cell adsorption, and wherein the first precursor material is a siloxane-based compound having a siloxane functional group with the SiOSi linkage, (3) placing a shadow mask having a predetermined pattern on the first plasma polymer layer thus formed, and (4) forming a second patterned plasma polymer layer by integrating a second precursor material using a plasma, wherein the second patterned plasma layer permits culturing of cells, whereby the patterned substrate is obtained.