Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.

Methods and compositions for extracting nucleic acids such as microRNAs (miRNAs) from biological samples are provided. Aspects of the methods include contacting a biological sample with proteinase K followed by contact with ferric oxide particles under acidic conditions to induce binding between the ferric oxide particles and nucleic acids (e.g., miRNAs) of the sample. In some cases, the ferric oxide particles are provided as part of a dissolvable film, which releases the ferric oxide particles upon solvation. In some embodiments, after nucleic acids bind to the ferric oxide particles, the particles are magnetically separated from the sample and are contacted with an alkaline elution buffer to release the nucleic acids.

Methods and compositions for extracting nucleic acids such as microRNAs (miRNAs) from biological samples are provided. Aspects of the methods include contacting a biological sample with proteinase K followed by contact with ferric oxide particles under acidic conditions to induce binding between the ferric oxide particles and nucleic acids (e.g., miRNAs) of the sample. In some cases, the ferric oxide particles are provided as part of a dissolvable film, which releases the ferric oxide particles upon solvation. In some embodiments, after nucleic acids bind to the ferric oxide particles, the particles are magnetically separated from the sample and are contacted with an alkaline elution buffer to release the nucleic acids.

Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.

Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided.

Provided herein are methods and systems for detection of nucleic acids for single cell samples. As part of the detection, a unique step of normalization of different single cell samples is included. One embodiment of the method includes i) selecting one or more target nucleic acid sequence of interest in an individual cell, where the target nucleic acid sequence is complementary to a nucleic acid in a cell; ii) providing a sample having a plurality of individual single cells and encapsulating one or more individual cell(s); iii) providing a sample normalization component to one or more encapsulated cell, where the normalization component comprises an exogenous nucleic acid having a known sequence; iv) providing nucleic acid primers for the target nucleic acid and the exogenous nucleic acid; v) providing a protease to each encapsulated cell and incubating the encapsulated cell with the protease in the drop to produce a cell lysate; vi) performing a nucleic acid amplification reaction to form an amplification product from the nucleic acid of a single cell, where the amplification product comprise amplicons of one or more target nucleic acid sequence and an amplicon for the exogenous nucleic acid; and vii) comparing the amplification products from the target amplicons and the exogenous nucleic acid amplicons and determining the copy number or sequence of the target nucleic acid in a single cell.

Provided herein are methods and systems for detection of nucleic acids for single cell samples. As part of the detection, a unique step of normalization of different single cell samples is included. One embodiment of the method includes i) selecting one or more target nucleic acid sequence of interest in an individual cell, where the target nucleic acid sequence is complementary to a nucleic acid in a cell; ii) providing a sample having a plurality of individual single cells and encapsulating one or more individual cell(s); iii) providing a sample normalization component to one or more encapsulated cell, where the normalization component comprises an exogenous nucleic acid having a known sequence; iv) providing nucleic acid primers for the target nucleic acid and the exogenous nucleic acid; v) providing a protease to each encapsulated cell and incubating the encapsulated cell with the protease in the drop to produce a cell lysate; vi) performing a nucleic acid amplification reaction to form an amplification product from the nucleic acid of a single cell, where the amplification product comprise amplicons of one or more target nucleic acid sequence and an amplicon for the exogenous nucleic acid; and vii) comparing the amplification products from the target amplicons and the exogenous nucleic acid amplicons and determining the copy number or sequence of the target nucleic acid in a single cell.

Provided herein are methods of increasing lipoprotein lipase (LPL) activity, by inhibiting apolipoprotein C3 (ApoCIII), which removes the ApoCIII inhibition of LPL, and permits VLDL to be converted to LDL. Also provided are methods for treating or preventing a lipid metabolism disorder, such as type 2 diabetes by use of an ApoCIII antagonist. Also provided are screening methods to identify ApoCIII antagonists.

Devices and methods are provided for collecting and handling difficult sample types.

Devices and methods are provided for collecting and handling difficult sample types.