Integrative DNA and RNA library preparations and uses thereof

A method for preparing targeted DNA and cDNA libraries in a same sample, comprising:

• (a) obtaining purified DNA and RNA from a same biological sample;
• (b) fragmenting the DNA and RNA;
• (c) polishing the ends of double-stranded DNA fragments for ligation;
• (d) polishing RNA fragments by polyadenylation;
• (e) ligating a DNA tag comprising a single-stranded portion to a 3′ end of the polished double-stranded DNA fragments in the same sample to form a tagged DNA, wherein the DNA tag comprises in a 5′ to 3′ direction a unique molecular identifier (UMI) and a DNA identifier;
• (f) performing reverse transcription of the polished RNA fragments in the same sample in the presence of a first RNA tag to form a tagged cDNA, wherein the first RNA tag comprises in a 5′ to 3′ direction a RNA identifier, a UMI, and a poly(T), and a second RNA tag, wherein the second RNA tag comprises in a 5′ to 3′ direction a RNA identifier, a UMI, and a template switching oligonucleotide (TSO);
• (g) amplifying the tagged DNA and tagged cDNA for enrichment with a set of gene specific primers to form an amplified sample;
• (h)
• further amplifying the first amplified sample with primers specific for the DNA tag;
• (i) further amplifying the amplified sample with primers specific for the RNA tag;
• and
• (j) generating the targeted DNA and cDNA libraries in the same sample.