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CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

ABSTRACT: CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

PROVIDER: PRJNA631718 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11768463.fastq.gz	Fastqsanger.gz
	SRR11768464.fastq.gz	Fastqsanger.gz
	SRR11768465.fastq.gz	Fastqsanger.gz
	SRR11768466.fastq.gz	Fastqsanger.gz
	SRR11768467.fastq.gz	Fastqsanger.gz

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CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Project description:Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach relying on nucleotide labeling by re-usable antibodies, but whether it is applicable to scRNA-seq, has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS. To assess the quality and performance of converted libraries, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and, after conversion, on a DNBSEQ-400RS. CoolMPS-derived results were in very high agreement with the Illumina dataset, and we demonstrate how technical variance between both technologies is significantly lower when compared to biological variance. Indeed, CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

2020-11-05 | GSE150284 | GEO

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.

Project description:Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

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