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Series GSE148090 Query DataSets for GSE148090
Status Public on Nov 10, 2021
Title Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types [organoids]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary High-throughput single-cell RNA-sequencing (scRNA-seq) has transformed our ability to resolve cellular properties across systems. A key scRNA-seq catalyzer was the introduction of microdroplet-based systems, which vastly improved sample handling and cell throughput. While powerful, the current microfluidic systems are limited to high cell density (>1000 cells) samples. This prevents the efficient processing of individual, small tissues or rare cells, leading to respectively confounded mosaic cell population read-outs or failed capture of diagnostically interesting cells. In this study, we developed a deterministic, mRNA-capture bead and cell co-encapsulation droplet system, DisCo, that overcomes these limitations by enabling precise particle position and droplet sorting control through combined machine-vision and multilayer microfluidics. We demonstrate that DisCo is capable of processing samples containing few cells (< 100 cells) at high efficiencies( >70%). To underscore the unique capabilities of DisCo, we mapped the developmental process of 31 individual intestinal organoids at the single cell level. This uncovered extensive cellular heterogeneity among organoids, revealing two so far uncharacterized organoid subtypes, “gobloids” and spheroids, predominantly consisting of respectively Muc2+ goblet and Ly6a+ stem cells. Further Disco data analysis thereby revealed strongly increased Yap1 target gene expression in these spheroids, suggesting mechano sensing as the underlying mechanism for their spontaneous formation. Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.Together, our novel “no-cell-left-behind” platform enables the deterministic processing of input cells, allowing high-resolution snapshots of cellular heterogeneity among rare cells or individual, small tissues or organoids.
 
Overall design Single intestinal organoids were processed at single-cell resolution using deterministic encapsulation of cells with mRNA capture beads.
 
Contributor(s) Bues J, Biočanin M, Pezoldt J, Dainese R, Chrisnandy A, Rezakhani S, Salen W, Gupta R, Amstad E, Claassen M, Lutolf M, Deplancke B
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Submission date Apr 05, 2020
Last update date Nov 12, 2021
Contact name Marjan Biočanin
E-mail(s) marjan.biocanin@epfl.ch
Organization name EPFL
Department SV-IBI
Lab Laboratory for systems biology and genetics/UPDE
Street address Station 19, SV 3820
City Lausanne
State/province Vaud
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (31)
GSM4453981 S0a
GSM4453982 S0b
GSM4453983 S0c
This SubSeries is part of SuperSeries:
GSE148093 Low-input, deterministic profiling of single-cell transcriptomes reveals individual intestinal organoid subtypes comprised of single, dominant cell types
Relations
BioProject PRJNA623194
SRA SRP255288

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
GSE148090_RAW.tar 5.8 Mb (http)(custom) TAR (of TXT)
GSE148090_SeuratObject_OrganoidKinetic.Rds.gz 13.0 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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