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.

Provided are a sequencing library and applications thereof. The provided sequencing library includes a first nucleic acid molecule and a second nucleic acid molecule. The first nucleic acid molecule carries a cell index sequence and a droplet index sequence. The second nucleic acid molecule carries an insert fragment and a cell index sequence.

Provided are a sequencing library and applications thereof. The provided sequencing library includes a first nucleic acid molecule and a second nucleic acid molecule. The first nucleic acid molecule carries a cell index sequence and a droplet index sequence. The second nucleic acid molecule carries an insert fragment and a cell index sequence.

Aspects of the present disclosure relate generally to methods, compositions, and kits for in situ whole cell barcoding. Aspects of the present disclosure also include a computer readable-medium and a processor to carry out the steps of the method described herein. In some embodiments, the disclosure relates to whole cell barcoding performed in situ.

Aspects of the present disclosure relate generally to methods, compositions, and kits for in situ whole cell barcoding. Aspects of the present disclosure also include a computer readable-medium and a processor to carry out the steps of the method described herein. In some embodiments, the disclosure relates to whole cell barcoding performed in situ.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.