Methods and compositions for combinatorial barcoding

A composition comprising a set of component barcodes for producing a set of combinatorial barcodes, comprising:

• n×m unique component barcodes, wherein n and m are positive integers, each of the component barcodes comprises:
• one of n unique barcode subunit sequences;
• and
• one or two linker sequences or the complements thereof,
• wherein the component barcodes are configured to connect to each other through the one or two linker sequences or the complements thereof to produce a set of combinatorial barcodes;
• and
• a plurality of solid supports,
• wherein a plurality of the component barcodes are attached to a solid support, wherein each of the component barcodes attached to the solid support comprise a first label, wherein component barcodes attached to the same solid support comprise the same first label, and wherein component barcodes attached to different solid supports comprise different first labels, and
• wherein each one of the set of combinatorial barcodes comprises:
• a first oligonucleotide and a second oligonucleotide, wherein the first oligonucleotide is attached to a solid support, wherein the second oligonucleotide is not attached to a solid support, wherein each of the first oligonucleotide and the second oligonucleotide comprises a target-specific region and at least one of n unique barcode subunit sequences, wherein the target-specific region of the first oligonucleotide is configured to bind the target, wherein the target-specific region of the second oligonucleotide is configured to bind a reverse complement of the target, and wherein only the target-specific region of the first oligonucleotide is oligo-dT, wherein the target comprises messenger RNA (mRNA).