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How RNA-Seq Contributes to Single-Cell Sequencing
June 20, 2024

How RNA-Seq Contributes to Single-Cell Sequencing

Table of Contents

How RNA-Seq Contributes to Single-Cell Sequencing

Genomics has evolved since the introduction of DNA sequencers in the 1990s. These technological advancements changed the way scientists work on genome research by presenting comprehensive genomic maps.

The sequencers have greatly improved aspects like speed, accuracy, sequencing depth, and read length over the past two decades. Out of numerous techniques, single-cell sequencing has gained remarkable recognition. Here, we focus on the role of RNA sequencing (RNA-Se­q) in single-cell sequencing and explore the complex mechanisms and applications of the  method. Understanding Single-Cell Sequencing and Single-Cell RNA Sequencing

Traditional next-generation sequencing (NGS) is similar to a group picture, but it can only offer an average representation of the group. In contrast, single-cell sequencing captures the uniqueness of each cell, like individual photos.

It helps reveal unique genetic markers and characteristics that might be missed by NGS. Single-cell sequencing is versatile, capable of analyzing different genetic components like genome (scDNA-seq), DNA-methylom­, and transcriptome (scRNA-seq) of individual cells.

For instance, single-cell RNA sequencing (scRNA-seq) works with the transcriptome to perceive RNA molecules in each cell. This provides a real-time view of active genes during cell sampling, offering a more in-depth look at gene expression studies.

The Process of Single-Cell Sequencing

The procedure of single-cell sequencing involves four key stages:

1.               Collecting Single Cells:

Techniques such as fluorescence activate­d cell sorting (FACS), magnetic-activated cell sorting (MACS), laser capture micro dissection (LCM), and manual cell picking help extract individual cells. The effectiveness, precision, and rate of cell recovery vary depending on samples and processes utilized.

2.               Harvesting, Sorting, and Augmenting Genetic Material:

After cell isolation, DNA or RNA is extracted, prepared, and enlarged. In scRNA-seq, mRNA molecules are enriched with poly [T]-primers, converted into cDNA via reverse transcriptase, and amplified. This ensures ample genetic material for subsequent sequencing.

3.               Creating a Sequencing Library:

The­ augmented DNA or cDNA forms a sequencing library. Unique barcodes are attached for each cell’s genetic profile, along with specific adapter sequences for the platform. This approach facilitates the combination of multiple libraries and the­ir simultaneous sequencing.

4.               Sequencing:

Prepared libraries are then sequenced with advanced platforms. Subtle differences exist in platform methods, but sequencing through synthesis like pyro sequencing and reversible terminator sequencing is commonly preferred. Sequencing generates data, allowing reconstitution of genetic content sequences from each cell.

Cell Isolation and Preliminary Sample­

Processing For successful single-cell sequencing, efficient cell separation is crucial. Common techniques include:

– Fluorescence Activated Cell Sorting (FACS):

It labels cells with fluorescent molecules linked to target antibodies. The selection parameters are diverse, but this me­thod can impact cell health and requires abundant starting cells.

– Magnetic-Activated Cell Sorting (MACS):

This technique employs ultra-magnetic particles to tag specific cell proteins. A magnetic field then isolates these marked ce­lls. The accuracy is contingent on antibody precision and alignment.

– Laser Capture­Micro dissection (LCM):

This technique segregates wanted cells from a solid tissue sample using a laser. It’s fast and reliable, but reliability requires visual identification of target cells. Also, laser treatment might disrupt DNA and RNA molecules.

– Manual Cell Picking (Micromanipulation):

This method uses micro-pipettes under a microscope to extract target cells. Its efficiency is limited and requires skilled professionals. Post isolation, the cells are lysed to confirm the quality of cell separation. The genetic matter is separated and increased to make enough for detection. The final product is single-strand DNA for scRNA-seq analysis due to the changing of RNA to cDNA.

Sequencing Library Preparation

When we build a sequencing library, we prepare single-strand DNA bits from a single cell’s genetics. With amplification, each DNA piece gets a unique barcode and special adapter sequences.

Thanks to the barcodes, you can mix different libraries in one sequencing run, making better use of your tools. Quality checks are important as well in the process. They make sure our library mirrors the first cell’s genetics.

You can check the DNA’s strength and cleanness after amplification, appraise RNA health for scRNA-se­q checks, and verify even genetic material boost.

The Lowdown on Sequencing Technology

Some sequencing tools use different methods, but synthesis is a popular choice. This method makes DNA pieces enlarge to form clones, which give off identical signals when sequenced. All this usually happens on a chip full of mini-wells.

Adapters and other molecules interact with the DNA particles here. The DNA picks up glow-in-the-dark nucleotides with each cycle. You can record the light they give off, which helps in figuring out the sequence.

Different ways to do sequencing exist.

One detects protons from base additions, another uses DNA ligases and glow tags for accuracy. Though, it ends up with short reads. When talking about single-cell sequencing, there are types to consider: – Single-Cell Genome Sequencing (scDNA-seq)

This type of sequencing looks at single cell genomes. This helps us learn about diversity in genes in micro biomes and cancer. Techniques like MDA and MALBAC are used for amplifying the DNA.

Single-Cell Transcriptome Sequencing (scRNA-seq):

The Single Cell Trancriptome Sequencing (SC RNA) sequence checks RNA molecules in each cell. This gives us knowledge about gene expression and regulation. Applications include pinpointing cellular subgroups, observing gene patterns, and looking at tumor diversity.

Single-Cell DNA Methylome­ Sequencing (scDNA-Met-se­q):

Single-Cell DNA Methylome­ Sequencing (scDNA-Met-se­q) helps in DNA methylation, which can influence gene activity. It’s used in development and cancer research, with bisulfite conversion commonly used to differentiate methylated and non-methylated cytosines.

Process of Data Analysis

 After sequencing, we process the raw output. We turn it into a file (BCL) and quality scores, then into a FASTQ file for more analysis. This file is lined up to a template genome, annotated, and studied to see variants and perform analyses.

Computational tools and packages, like Bio conductor for R language, are out there to help. Single cell sequencing data analysis involves several steps.

·        First, data normalization, PCA, t-SNE analysis, cluster analysis, then pathway or gene set enrichment analyses. These identify patterns and biological behaviour in our data. Single-cell sequencing lets us study individual cells. It reveals their specific contributions to an organism’s physiology or pathology. This is great for studying rare cells and exploring phenotypic variations within cell populations.

·        This helps in discovering rare antigen-specific T or B cells, studying human micro biomes, exploring chemo resistant tumor subpopulations, figuring out gene functions in plant tissue, prognostics, and intra-tumor cellular heterogeneity.

·        The combo of single cell sequencing and other techniques gives us a broader view of genetic, epigenetic, and transcriptomic landscapes in a cellular population. This can reveal more subpopulations and infer functional connections between observed alterations.

·        However, integrating multiomics data poses challenge­s, particularly in developing adequate computational methods for data analysis. RNA-Seq has lifted single cell sequencing to a new level. It gives a deep look into cellular heterogeneity, gene regulation, and biological systems.


RNA-Seq has helped in the growth of single-cell sequencing, letting scientists explore gene behavior more intensely than ever before. Deep understanding obtained from inspecting each individual RNA sequence helps to grasp cell diversity, gene control, and mechanism of biological systems.


The process of single cell RNA sequencing is invaluable. In future, the applications of single-cell sequencing technologies will expand, opening more door to scie­ntific discovery and medical research.

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