Provided herein are oligomers, compositions, kits, and methods for capturing target polynucleotides, e.g., for downstream applications such as amplification, library preparation, or sequencing. In some embodiments, a capture oligomer is provided or used that comprises a capture sequence that is annealed to a complement that prevents capture until the complement is displaced in a target-polynucleotide dependent manner. In some embodiments, an amount of target polynucleotide is captured that is less than or equal to a predetermined amount.

Provided herein are oligomers, compositions, kits, and methods for capturing target polynucleotides, e.g., for downstream applications such as amplification, library preparation, or sequencing. In some embodiments, a capture oligomer is provided or used that comprises a capture sequence that is annealed to a complement that prevents capture until the complement is displaced in a target-polynucleotide dependent manner. In some embodiments, an amount of target polynucleotide is captured that is less than or equal to a predetermined amount.

Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.

Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.

This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.

This disclosure describes a technique for performing random access in a pool of polynucleotides by using one unique primer and one homopolymer primer to selectively amplify some but not all of the polynucleotides in the pool. The polynucleotides are synthesized by a template independent polymerase such as terminal deoxynucleotide transferase (TdT) rather than by phosphoramidite synthesis. Enzymatic synthesis efficiently creates homopolymer sequences through unregulated synthesis. Use of one homopolymer primer instead of two unique primers decreases the complexity, time, and cost of synthesizing the polynucleotides. Use of a unique primer provides a sequence that can be varied to uniquely identify multiple different groups of polynucleotides. This enables random access by polymerase chain reaction (PCR) amplification while still benefitting from the efficiency of homopolymer synthesis. The polynucleotides may include payload regions that use a sequence of nucleotides to encode digital data.

Provided are immune cell RNA sequencing methods. In some embodiments, the methods comprise producing a circularized DNA comprising a complementary DNA (cDNA) and a known heterologous sequence, wherein the cDNA is produced from an immune cell RNA. Such methods further comprise performing rolling circle amplification using the circularized DNA as template to produce a concatemer comprising repeating segments comprising the cDNA and the known heterologous sequence. Such methods further comprise sequencing the concatemer or fragments thereof. Also provided are methods comprising producing immune cell RNA sequencing reads using a R2C2 sequencing method, extracting HLA reads from the sequencing reads, and producing allele-specific HLA sequences from the extracted HLA reads. Also provided are computer-readable media, systems, compositions and kits that find use, e.g., in practicing the methods of the present disclosure.

Provided are immune cell RNA sequencing methods. In some embodiments, the methods comprise producing a circularized DNA comprising a complementary DNA (cDNA) and a known heterologous sequence, wherein the cDNA is produced from an immune cell RNA. Such methods further comprise performing rolling circle amplification using the circularized DNA as template to produce a concatemer comprising repeating segments comprising the cDNA and the known heterologous sequence. Such methods further comprise sequencing the concatemer or fragments thereof. Also provided are methods comprising producing immune cell RNA sequencing reads using a R2C2 sequencing method, extracting HLA reads from the sequencing reads, and producing allele-specific HLA sequences from the extracted HLA reads. Also provided are computer-readable media, systems, compositions and kits that find use, e.g., in practicing the methods of the present disclosure.

Provided herein are methods for labeling input DNA with oligonucleotide barcode sequences, and selective PCR amplification of DNA sequence variants across the targeted regions for variant quantitation.

Provided herein are methods for labeling input DNA with oligonucleotide barcode sequences, and selective PCR amplification of DNA sequence variants across the targeted regions for variant quantitation.