Genomics

Dataset Information

0

Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types


ABSTRACT: Single-nuclei RNA-Seq is widely employed to investigate cell types, especially of human brain and frozen samples. In contrast to single-cell approaches, many single-nuclei reads are purely intronic. Here, using microfluidics, PCR-based artifact removal, target enrichment, and long-read sequencing, we developed single-nuclei isoform RNA-sequencing (‘SnISOr-Seq’), and applied it to human adult frontal cortex. SnISOr-Seq dramatically increased the fraction of informative reads. We found that exons associated with autism exhibit coordinated and highly cell-type specific inclusion. We discovered two distinct combination patterns: first, those distinguishing neural cell types, enriched in TSS-exon, exon-polyA-site, and non-adjacent exon pairs. Second, those with multiple configurations within one cell type, enriched in adjacent exon pairs. Furthermore, adjacent exons are predominantly mutually-associated, while distant exons are frequently mutually-exclusive. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons. SnISOr-Seq enables single-nuclei long-read isoform analysis in human brain, and in any frozen or hard-to-dissociate sample.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE178175 | GEO | 2022/01/16

REPOSITORIES: GEO

Similar Datasets

2021-02-02 | PXD023373 | Pride
2011-09-14 | E-GEOD-30995 | biostudies-arrayexpress
2013-09-06 | E-GEOD-47032 | biostudies-arrayexpress
2016-07-03 | E-GEOD-71178 | biostudies-arrayexpress
2008-08-15 | E-GEOD-11863 | biostudies-arrayexpress
2017-01-01 | GSE76026 | GEO
2020-05-17 | GSE138362 | GEO
2015-12-10 | E-GEOD-65999 | biostudies-arrayexpress
2015-05-20 | PXD001449 | Pride
2014-08-12 | GSE60254 | GEO