High-throughput full-length single-cell RNA-seq automation

Mamanova, Lira; Miao, Zhichao; Jinat, Ayesha; Ellis, Peter; Shirley, Lesley; Teichmann, Sarah A.

doi:10.1038/s41596-021-00523-3

Cited by 15 publications

(13 citation statements)

References 56 publications

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“…We leveraged a full-length SMART-Seq technology which amplifies from both 3 0 and 5 0 ends to interrogate the compositional differences in WAT when comparing: 1) whole adipose tissue snRNA-Seq, 2) isolated adipocytes snRNA-Seq, and 3) SVF scRNA-Seq. This approach and level of sc/snRNA-Seq benefits the capture of more mapped transcript reads (Mamanova et al, 2021), i.e. enhanced gene coverage, that has specifically been applied in this study and significantly extends previous sc-and snRNA-Seq findings in WAT.…”

Section: Introductionsupporting

confidence: 68%

Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations

et al. 2022

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Section: Introductionsupporting

confidence: 68%

Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations

et al. 2022

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“…There is a range of scRNAseq methods available with different benefits for studying mucosal immunology 25 – 28 . Platforms relying on the isolation of dissociated cells by fluorescence-activated cell sorting (FACS) or microfluidic devices include STRT-seq 29 , CEL2-seq 30 , MARS-seq 31 and SMART-seq2-3 32 – 34 . Use of FACS provides auxiliary information of proteins targeted by a select panel of fluorophore-tagged antibodies and can help unite transcriptional profiles to traditional cell type identities.…”

Section: Scrnaseq Approaches To Studying Intestinal Immunitymentioning

confidence: 99%

Redefining intestinal immunity with single-cell transcriptomics

et al. 2022

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The intestinal immune system represents the largest collection of immune cells in the body and is continually exposed to antigens from food and the microbiota. Here we discuss the contribution of single-cell transcriptomics in shaping our understanding of this complex system. We consider the impact on resolving early intestine development, engagement with the neighbouring microbiota, diversity of intestinal immune cells, compartmentalisation within the intestines and interactions with non-immune cells. Finally, we offer a perspective on open questions about gut immunity that evolving single-cell technologies are well placed to address.

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“…RNAseq-libraries were prepared from 6 samples per each genotype, reporter control- Ai14 and Isl1CKO-Ai14 mutant, and each sample contained 100 tdTomato + neurons. Following the manufacturer’s instructions, the NEB Next single-cell low input RNA library prep kit for Illumina was used for cDNA synthesis, amplification, and library generation 99 at the Gene Core Facility (Institute of Biotechnology CAS, Czechia). Fragment Analyzer assessed the quality of cDNA libraries.…”

Section: Methodsmentioning

confidence: 99%

ISL1 is necessary for auditory neuron development and contributes towards tonotopic organization

Filova

Pysanenko

Tavakoli

et al. 2021

Preprint

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A cardinal feature of the auditory pathway is frequency selectivity, represented in the form of a tonotopic map from the cochlea to the cortex. The molecular determinants of the auditory frequency map are unknown. Here, we discovered that the transcription factor ISL1 regulates molecular and cellular features of auditory neurons, including the formation of the spiral ganglion, and peripheral and central processes that shape the tonotopic representation of the auditory map. We selectively knocked out Isl1 in auditory neurons using Neurod1Cre strategies. In the absence of Isl1, spiral ganglion neurons migrate into the central cochlea and beyond, and the cochlear wiring is profoundly reduced and disrupted. The central axons of Isl1 mutants lose their topographic projections and segregation at the cochlear nucleus. Transcriptome analysis of spiral ganglion neurons shows that Isl1 regulates neurogenesis, axonogenesis, migration, neurotransmission-related machinery, and synaptic communication patterns. We show that peripheral disorganization in the cochlea affects the physiological properties of hearing in the midbrain and auditory behavior. Surprisingly, auditory processing features are preserved despite the significant hearing impairment, revealing central auditory pathway resilience and plasticity in Isl1 mutant mice. Mutant mice have a reduced acoustic startle reflex, altered prepulse inhibition, and characteristics of compensatory neural hyperactivity centrally. Our findings show that ISL1 is one of the obligatory factors required to sculpt auditory structural and functional tonotopic maps. Still, upon Isl1 deletion, the ensuing central compensatory plasticity of the auditory pathway does not suffice to overcome developmentally induced peripheral dysfunction of the cochlea.

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High-throughput full-length single-cell RNA-seq automation

Cited by 15 publications

References 56 publications

Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations

Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations

Redefining intestinal immunity with single-cell transcriptomics

ISL1 is necessary for auditory neuron development and contributes towards tonotopic organization

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