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Series GSE208156 Query DataSets for GSE208156
Status Public on Jul 02, 2023
Title spinDrop: a modular droplet microfluidic platform to maximise single-cell RNA sequencing information content
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Droplet microfluidic methods have massively increased the throughput of single-cell RNA sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples as well as lower overall RNA capture efficiency. These drawbacks stem from the lack of strategies to enrich for high-quality material at the moment of cell encapsulation and the lack of implementable multi-step enzymatic processes that increase RNA capture. Here we alleviate both bottlenecks by deploying fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei or fixed cells and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half, depending on sample quality. We harness these unique properties to deliver a high-quality molecular atlas of mouse brain development using highly damaged input material. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
Overall design Mouse ES, HEK293T cells and mouse embryonic brain sections at stage E10.5 were dissociated and processed for single-cell RNA-sequencing using the spinDrop workflow.
Web link
Contributor(s) De Jonghe J, Kaminski T, Hollfelder F
Citation(s) 37553326
Submission date Jul 13, 2022
Last update date Aug 21, 2023
Contact name Florian Hollfelder
Organization name University of Cambridge
Street address 80 tennis court road
City Cambridge
ZIP/Postal code CB21GA
Country United Kingdom
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (16)
GSM6338230 spindrop PFA fixed HEK293T
GSM6338231 spindrop peg HEK293T
GSM6338232 spindrop no peg HEK293T
BioProject PRJNA858488

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE208156_EU_E85_nascent_matrix.csv.gz 1.1 Mb (ftp)(http) CSV
GSE208156_EU_E85_old_matrix.csv.gz 2.9 Mb (ftp)(http) CSV
GSE208156_FADS_PBMC_matrix.csv.gz 232.4 Kb (ftp)(http) CSV
GSE208156_RAW.tar 28.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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