There is disclosed a method for whole genome amplification and analysis of multiple target molecules in a biological sample including genomic DNA and target molecules comprising the steps of contacting the biological sample with at least one binding agent, directed to at least one of the target molecules, conjugated with a tagged oligonucleotide, which comprises a binding-agent barcode sequence (BAB) and a unique molecular identifier sequence (UMI); carrying out a separating step to selectively remove unbound binding agent thus obtaining a labeled biological sample; simultaneously carrying out on the labeled biological sample a whole genome amplification and an amplification of the tagged oligonucleotide; preparing a massively parallel sequencing library from the amplified tagged oligonucleotide; sequencing the massively parallel sequencing library; retrieving the sequences of the BAB and UMI from each sequencing read; counting the number of distinct UMI for each binding agent.

There is disclosed a method for whole genome amplification and analysis of multiple target molecules in a biological sample including genomic DNA and target molecules comprising the steps of contacting the biological sample with at least one binding agent, directed to at least one of the target molecules, conjugated with a tagged oligonucleotide, which comprises a binding-agent barcode sequence (BAB) and a unique molecular identifier sequence (UMI); carrying out a separating step to selectively remove unbound binding agent thus obtaining a labeled biological sample; simultaneously carrying out on the labeled biological sample a whole genome amplification and an amplification of the tagged oligonucleotide; preparing a massively parallel sequencing library from the amplified tagged oligonucleotide; sequencing the massively parallel sequencing library; retrieving the sequences of the BAB and UMI from each sequencing read; counting the number of distinct UMI for each binding agent.

Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.

Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.

Compositions and methods for identifying and using cis-regulatory and decoy sequences are disclosed.

Compositions and methods for identifying and using cis-regulatory and decoy sequences are disclosed.

The technology relates in part to methods and compositions for analyzing nucleic acid. In some aspects, the technology relates to methods and compositions for preparing a nucleic acid library from single-stranded nucleic acid fragments.

The technology relates in part to methods and compositions for analyzing nucleic acid. In some aspects, the technology relates to methods and compositions for preparing a nucleic acid library from single-stranded nucleic acid fragments.

The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5′ to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5′ flap containing one or more nucleotides at its 3′ end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribonucleotide. Probes for use in the detection methods are provided.

The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5′ to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5′ flap containing one or more nucleotides at its 3′ end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribonucleotide. Probes for use in the detection methods are provided.