The disclosure provides for methods, compositions, systems, devices, and kits for whole transcriptome amplification using stochastic barcodes.

Provided herein, in some embodiments, are methods of purifying a nucleic acid preparation. The methods may comprise contacting a nucleic acid preparation comprising messenger ribonucleic acid with an RNase III enzyme that is immobilized on a solid support and binds to double-stranded RNA contaminants.

Provided herein, in some embodiments, are methods of purifying a nucleic acid preparation. The methods may comprise contacting a nucleic acid preparation comprising messenger ribonucleic acid with an RNase III enzyme that is immobilized on a solid support and binds to double-stranded RNA contaminants.

The present invention relates to methods for identifying and/or quantifying low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.

The present invention relates to methods for identifying and/or quantifying low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.

The invention provides compositions and methods allowing for rapid, accurate, robust, and low-cost diagnosis of infectious diseases via extraction-free, direct PCR techniques.

The invention provides compositions and methods allowing for rapid, accurate, robust, and low-cost diagnosis of infectious diseases via extraction-free, direct PCR techniques.

Disclosed is a method for isolating, amplifying, and sequencing infectious agents' nucleic acids from an acellular fraction of a biological fluid using detergents and nucleic acids-digesting enzymes. Also disclosed is a kit-of-parts including detergents and nucleic acids-digesting enzymes for the implementation of the methods described.

Disclosed is a method for isolating, amplifying, and sequencing infectious agents' nucleic acids from an acellular fraction of a biological fluid using detergents and nucleic acids-digesting enzymes. Also disclosed is a kit-of-parts including detergents and nucleic acids-digesting enzymes for the implementation of the methods described.

Provided herein are methods for spatial analysis using targeted RNA depletion.