Method and system for 3d reconstruction of tissue gene expression data

A method for the computer-implemented analysis of spatial abundance of poly-A containing RNA in a tissue sample, comprising the steps of:

• i) obtaining
• (i1) imaging data of a plurality of consecutive sections of said tissue sample, and
• (i2) two-dimensional sequencing data of said poly-A containing RNA in said sections,
• ii) registering the imaging data and detecting the two-dimensional position of beads in said imaging data, and employing a first machine learning method to obtain a first barcode set from the imaging data,
• iii) processing the two-dimensional sequencing data to obtain a second barcode set from the sequencing data,
• iv) processing the first and second barcode sets by an optimal transport framework and/or supervised machine learning to match the data sets to each other and to obtain matched barcodes,
• v) outputting based on the matched barcodes a matrix holding the expression values for each gene that was identified in each bead found in the data.

A method for analyzing spatial abundance of poly-A containing RNA in a tissue sample from a subject, comprising the steps of

• (a) providing a plurality of consecutive sections of said tissue sample,
• (b) producing a plurality of array structures by depositing for each array structure beads with an average diameter of from 1 to 100 μm on a solid support,
• wherein each bead comprises at least 1000 attached oligonucleotides and wherein each of the at least 1000 attached oligonucleotides of each bead comprises:
• (i) a bead identification sequence that is common to all at least 1000 oligonucleotides on each bead and that is unique to each bead in the respective array structure, and
• (ii) a poly-T sequence to capture mRNA molecules in said sample,
• (c) identifying for each array structure the bead identification sequence and associated two-dimensional position on the solid support of individual beads of the beads deposited on the solid support by performing a sequence-by-synthesis technique using a microscope,
• (d) contacting each array structure of the plurality of array structures with a section of the plurality of sections of said tissue sample and permeabilizing the tissue sections, thereby capturing poly-A containing RNA in said sample by said oligonucleotides attached to the beads,
• (e) sequencing for each array structure the RNA molecules bound to the oligonucleotides of the beads and the associated bead identification sequence for each RNA sequenced,
• (f) matching for each array structure the bead identification sequence determined in steps (c) and (e) wherein a two-dimensional position in the array structure is assigned to the nucleotide sequence of each captured RNA,
• (g) aligning the two-dimensional sequence data obtained in step (f) for consecutive sections thereby obtaining spatially-resolvable RNA abundance data from the tissue sample, wherein said aligning comprises performing a transformation on one or more reference of poly-A containing RNAs in the two-dimensional sequence data obtained in step (f) for consecutive sections.