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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Jan 7, 2026

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress.

Koen Deserranno1, Elise Callens1, Danique Berrevoet1

  • 1Laboratory of Pharmaceutical Biotechnology - NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, BLOK A, FLOOR3, Ghent, 9000, Belgium.

BMC Genomics
|December 6, 2025
PubMed
Summary

A new plate-based method (PB10X) enhances single-cell RNA sequencing (scRNA-seq) compatibility with 10X Genomics technology. This cost-effective approach improves immune receptor repertoire sequencing and gene expression profiling, especially for small cell populations.

Keywords:
10X GenomicsBenchmarkingIndexed sortingPlate-based scRNA-seqSmart-seq

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Area of Science:

  • Single-cell transcriptomics
  • Genomics
  • Immunology

Background:

  • 10X Genomics (10X) is a leading single-cell RNA-sequencing (scRNA-seq) technology for gene expression and T-cell receptor (TCR) profiling.
  • Its microfluidics-based approach limits direct pairing of indexed sorting with scRNA-seq data and is costly for small cell populations.

Purpose of the Study:

  • To develop a plate-based, 10X-compatible (PB10X) scRNA-seq strategy.
  • To overcome the limitations of existing microfluidics-based scRNA-seq methods for cost-effective profiling of small cell samples.

Main Methods:

  • Developed a plate-based, 10X-compatible (PB10X) scRNA-seq strategy based on the Smart-seq3xpress (SS3X) principle.
  • Utilized Fluorescence Activated Cell Sorting (FACS) for indexed sorting directly into 384-well plates.
  • Generated cDNA compatible with 10X Single Cell 5' library kits (V(D)J and Gene Expression).

Main Results:

  • PB10X demonstrated high performance in V(D)J and gene expression profiling on Jurkat lymphoblasts.
  • Achieved paired TCRαβ chain sequencing for 81.71% of cells at limited sequencing depth.
  • Detected a mean of 4,343 genes and 16,137 UMIs per cell, with high uniquely mapped reads and protein-coding genes.
  • Resolved the strand invasion artifact observed in SS3X.

Conclusions:

  • The novel PB10X method provides cost-effective, plate-based 10X-compatible immune receptor repertoire and gene expression profiling.
  • PB10X is a promising single-cell transcriptomics strategy, particularly for immunological studies with limited cell numbers.