Compositions and methods for labeling target nucleic acid molecules

A method, comprising:

• (a) hybridizing a primer to a library of polynucleotide molecules comprising, in 3′ to 5′ order, a first adapter, a sequence derived from genomic DNA, cDNA or RNA, and a second adapter, wherein the primer hybridizes to the first adaptor;
• (b) extending the 3′ end of the hybridized primer to produce primer extension products;
• (c) hybridizing the primer extension products with synthetic oligonucleotides, wherein:
• (i) the synthetic oligonucleotides comprise, in 3′ to 5′ order, a non-extendable 3′ end, a hybridization sequence, and a variable barcode sequence;
• and
• (ii) the hybridization sequence hybridizes to a 3′ terminal region of the sequence complementary to the second adapter;
• and
• (d) incubating the hybridized primer extension products of step (b) with a polymerase such that the polymerase extends the 3′ end of the primer extension products to form a further extended primer extension product.