METHOD OF SPATIAL SEQUENCING OF GENES FROM TISSUE USING PADLOCKS WITH GAPS ON SUBSTRATE

The invention is directed to a method to obtain the spatial location and sequence information of a target sequence in a sample comprising at least one m-RNA strand comprising the stepsa. providing a surface with a plurality of spacer units capable of binding at least one m-RNA strand and with at least one fiducial markerb. providing a sample comprising at least one m-RNA strand to the surface wherein at least one m-RNA strand of the sample binds to at least one spacer unit creating at least one single stranded oligomerc. taking a first image of the surface to obtain the spatial information of the sample relative to the fiducial markerd. removing sample form surfacee. hybridizing at least one oligonucleotide comprising 50 - 1000 nucleic acids with its 5' and 3' ends to complementary parts of the single stranded oligomer thereby forming a padlock-shaped structure that is ligated to create a single strand circular templatef. multiplying the single strand circular template by a polymerase capable of rolling circle amplification into a plurality of DNA concatemers thereby forming roloniesg. obtaining the sequence information of the roloniesh. linking the spatial information of the sample with the sequence information of the rolonies.