This invention provides methods for detecting RNAs in a biological sample while using only a small amount of sample input, e.g., less than or equal to 1 mL. The methods described herein are able to detect a large percentage of protein-coding genes having the ENSEMBL gene annotation HG38.

Methods and compositions to minimize barcode exchange during the preparation of barcoded next-generation sequencing libraries prepared from a single cell. The methods utilize oligonucleotides containing a 3-terminated blocking group or sequences that prevent amplification or extension.

A method of determining the susceptibility of a cancer in a subject to treatment with an antimetabolite includes obtaining a sample of cancer cells from the subject, measuring the level of UDG expression in the cancer cells, and comparing the measured levels of UDG expression in the cancer cells to a control level.

The present disclosure provides, among other things, a way to amplify and sequence target sequences in a low-input sample. In some embodiments, the method comprises ligating a double-stranded adaptor onto a population of fragments to produce tagged fragments, and linearly amplifying the tagged fragments.

Proposed are an adenine base editor having increased thymine-cytosine sequence-specific cytosine base editing activity, a cytosine base editing method, and a cytosine base editing kit. The editor, produced by introducing a P48R mutation into an adenosine deaminase, has an operating range that is more sophisticated than conventional cytosine base editors, allows cytosine base editing only when cytosine is positioned right behind thymine, thereby enabling elaborate editing even when there is a plurality of cytosines within the range, and enables cytosine to be substituted with thymine or guanine in the presence or absence of UGI, respectively. Therefore, the cytosine base editing composition can be effectively used in the fields of gene therapy or new crop development which requires precise editing of only cytosine in all living organisms, including humans, plants, and bacteria.

Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.

The present invention relates to polypeptides comprising a GH39 glycosyl hydrolase domain and polynucleotides encoding the polypeptides. The invention further relates to compositions comprising such polypeptides such as cleaning compositions, use of polypeptides comprising the GH39 domain in cleaning processes. The invention further relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Some aspects of this disclosure provide compositions, strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. In some embodiments, fusion proteins capable of inducing a cytosine (C) to guanine (G) change in a nucleic acid (e.g., genomic DNA) are provided. In some embodiments, fusion proteins of a nucleic acid programmable DNA binding protein (e.g., Cas9) and nucleic acid editing proteins or protein domains, e.g., deaminase domains, polymerase domains, and/or base excision enzymes are provided. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, reagents and kits for the generation of targeted nucleic acid editing proteins, e.g., fusion proteins of a nucleic acid programmable DNA binding protein (e.g., Cas9), and nucleic acid editing proteins or domains, are provided.

The present invention relates to the analysis of complex single cell sequencing libraries. Disclosed are methods for enrichment of library members based on the presence of cell-of origin barcodes to identify and concentrate DNA that is relevant to interesting cells or components that would be expensive or difficult to study otherwise. Also, disclosed are methods of capturing cDNA library molecules by use of CRISPR systems, hybridization or PCR. The present invention allows for identifying the properties of rare cells in single cell RNA-seq data and accurately profile them through clustering approaches. Further information on transcript abundances from subpopulations of single cells can be analyzed at a lower sequencing effort. The methods also allow for linking TCR alpha and beta chains at the single cell level.

The subject invention provides microbe-based products, as well as their use in simultaneously enhancing oil recovery from an oil well while efficiently removing contaminating compositions such as biofilm, scale, paraffin, and/or asphaltenes from oil production equipment and oil-bearing formations. The subject invention can also be used to disperse paraffin and asphaltene precipitates, and to reduce the viscosity of heavy crude oil. The subject invention further provides materials and methods for bioremediation of hydrocarbon-contaminated sites.