Study

Single-nucleus transcriptomic profiling of aging Down Syndrome brains

Study ID Alternative Stable ID Type
EGAS00001005691 Other

Study Description

Down syndrome (DS) – trisomy of human chromosome 21 (HSA21) – is characterized by lifelong cognitive impairments and development of neuropathological hallmarks of Alzheimer’s disease (AD). The cellular and molecular modifications responsible for these effects are not understood. Here we performed single-nucleus RNA-sequencing (snRNA-seq) employing both short (Illumina) and long-read (Pacific Biosciences) sequencing technologies on a total of 29 DS and non-DS control prefrontal cortex samples. In DS, the ratio of inhibitory-to-excitatory neurons was significantly increased, which was not observed in previous reports examining sporadic AD. DS microglial transcriptomes displayed AD-related aging and activation signatures in advance of AD neuropathology, with increased microglial expression of C1q complement genes (associated with dendritic pruning) and the HSA21 transcription factor gene RUNX1. Long-read sequencing detected vast RNA isoform diversity within and amongst specific cell types including numerous novel sequences that differed between DS and normal brains. Notably, ... (Show More)

Study Datasets 5 datasets.

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Dataset ID Description Technology Samples
EGAD00001008284
16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for APP using custom designed primers.
Sequel 16
EGAD00001008285
16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for SPP1 using custom designed primers.
Sequel 16
EGAD00001008286
16 DS and Control brains samples were prepared using the 10X Genomics Single Cell 3' v3 kit. Pre-fragmented cDNA libraries were loaded onto a Pacific Biosciences Sequel II to sequence single-nucleus isoforms.
Sequel 16
EGAD00001008287
29 DS and Control brain samples were prepared using the 10X Genomics Single Cell 3' v3 kit. The cDNA libraries were sequenced on an Illumina Novaseq 6000.
Illumina NovaSeq 6000 29
EGAD00001008288
16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for BIN1 using custom designed primers.
Sequel 16

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