Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.

RNA isoform diversity, produced via alternative splicing, and alternative usage of transcription start and poly(A) sites, results in varied transcripts being derived from the same gene. Distinct isoforms can play important biological roles, including by changing the sequences or expression levels of protein products. The first single-cell approaches to RNA sequencing-and later, spatial approaches-which are now widely used for the identification of differentially expressed genes, rely on short reads and offer the ability to transcriptomically compare different cell types but are limited in their ability to measure differential isoform expression.

ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease.

Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether chromatin and splicing alterations in the brain convergently affect the same cell types or divergently different ones.

Ariadne: synthetic long read deconvolution using assembly graphs.

Synthetic long read sequencing techniques such as UST's TELL-Seq and Loop Genomics' LoopSeq combine 3[Formula: see text] barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3[Formula: see text] unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.

Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.

Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq).