Use of droplet single cell epigenome profiling for patient stratification

An aspect of the invention relates to a method for the diagnosis and/or prognosis of drug resistance, wherein single cell chromatin states are profiled in cells obtained from a subject by using a microfluidic system, the method comprising the steps of: a. providing at least a droplet of first type, wherein said droplet of first type comprises i. a biological element, ii. a lysis buffer, and iii. a nuclease, b. collecting said droplet of first type under conditions that temporarily inactivate said nuclease, c. incubating said droplet of first type, thereby reactivating said nuclease, d. providing at least a droplet of second type, wherein said droplet of second type comprises a nucleic acid sequence, e. merging said droplets of first and second type, thereby generating a droplet of third type, f. incubating said droplet of third type, thereby linking said nucleic acid sequence to one or more genomic region(s) of interest, g. sequencing said one or more genomic region(s) of interest. A further aspect of the present invention relates to a nucleic acid sequence comprising: a. at least one index sequence, b. a sequencing adaptor, and c. at least one protecting function positioned at 3'- and/or 5'-end.