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In the field of
cellular biology
Cell biology (also cellular biology or cytology) is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and ...
, single-cell analysis is the study of
genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
,
transcriptomics
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. He ...
,
proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...
,
metabolomics
Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...
and
cell–cell interaction Cell–cell interaction refers to the direct interactions between cell surfaces that play a crucial role in the development and function of multicellular organisms.
These interactions allow cells to communicate with each other in response to changes ...
s at the single cell level.
The concept of single-cell analysis originated in the 1970s. Before the discovery of heterogeneity, single-cell analysis mainly referred to the analysis or manipulation of an individual cell in a bulk population of cells at a particular condition using optical or electronic microscope. To date, due to the heterogeneity seen in both eukaryotic and prokaryotic cell populations, analyzing a single cell makes it possible to discover mechanisms not seen when studying a bulk population of cells. Technologies such as
fluorescence-activated cell sorting
Flow cytometry (FC) is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles.
In this process, a sample containing cells or particles is suspended in a fluid and injected into the flo ...
(FACS) allow the precise isolation of selected single cells from complex samples, while high throughput single cell partitioning technologies, enable the simultaneous molecular analysis of hundreds or thousands of single unsorted cells; this is particularly useful for the analysis of transcriptome variation in genotypically identical cells, allowing the definition of otherwise undetectable cell subtypes. The development of new technologies is increasing our ability to analyze the genome and transcriptome of single cells, as well as to quantify their proteome and
metabolome
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The smal ...
.
Mass spectrometry techniques have become important analytical tools for proteomic and metabolomic analysis of single cells.
Recent advances have enabled quantifying thousands of protein across hundreds of single cells, and thus make possible new types of analysis.
In situ sequencing and
fluorescence in situ hybridization
Fluorescence ''in situ'' hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence complementarity. It was developed b ...
(FISH) do not require that cells be isolated and are increasingly being used for analysis of tissues.
Single-cell isolation
Many single-cell analysis techniques require the isolation of individual cells. Methods currently used for single cell isolation include: Dielectrophoretic digital sorting, enzymatic digestion,
FACS, hydrodynamic traps,
laser capture microdissection
Laser capture microdissection (LCM), also called microdissection, laser microdissection (LMD), or laser-assisted microdissection (LMD or LAM), is a method for isolating specific cells of interest from microscopic regions of tissue/cells/organisms ...
, manual picking,
microfluidics
Microfluidics refers to the behavior, precise control, and manipulation of fluids that are geometrically constrained to a small scale (typically sub-millimeter) at which surface forces dominate volumetric forces. It is a multidisciplinary field tha ...
,
micromanipulation
A micromanipulator is a device which is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. It may typically consist of an input joysti ...
,
serial dilution
A serial dilution is the stepwise dilution of a substance in solution. Usually the dilution factor at each step is constant, resulting in a geometric progression of the concentration in a logarithmic fashion. A ten-fold serial dilution could be 1 ...
, and Raman tweezers.
Manual single cell picking is a method where cells in a suspension are viewed under a microscope, and individually picked using a
micropipette
A pipette (sometimes spelled as pipett) is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. Pipettes come in several designs for various purposes with diffe ...
.
Raman tweezers is a technique where
Raman spectroscopy
Raman spectroscopy () (named after Indian physicist C. V. Raman) is a spectroscopic technique typically used to determine vibrational modes of molecules, although rotational and other low-frequency modes of systems may also be observed. Raman sp ...
is combined with
optical tweezers
Optical tweezers (originally called single-beam gradient force trap) are scientific instruments that use a highly focused laser beam to hold and move microscopic and sub-microscopic objects like atoms, nanoparticles and droplets, in a manner simila ...
, which uses a laser beam to trap, and manipulate cells.
The Dielectrophoretic digital sorting method utilizes a semiconductor controlled array of electrodes in a microfluidic chip to trap single cells in Dielectrophoretic (DEP) cages. Cell identification is ensured by the combination of fluorescent markers with image observation. Precision delivery is ensured by the semiconductor controlled motion of DEP cages in the flow cell.
The development of hydrodynamic-based microfluidic biochips has been increasing over the years. In this technique, the cells or particles are trapped in a particular region for single cell analysis (SCA) usually without any application of external force fields such as optical, electrical, magnetic or acoustic. There is a need to explore the insights of SCA in the cell's natural state and development of these techniques is highly essential for that study. Researchers have highlighted the vast potential field that needs to be explored to develop biochip devices to suit market/researcher demands. Hydrodynamic microfluidics facilitates the development of passive lab-on-chip applications. A latest review gives an account of the recent advances in this field, along with their mechanisms, methods and applications.
Associated Technologies
Dielectrophoretic digital sorting method utilizes a semiconductor controlled array of electrodes in a microfluidic chip to trap single cells in Dielectrophoretic (DEP) cages. Cell identification is ensured by the combination of fluorescent markers with image observation. Precision delivery is ensured by the semiconductor controlled motion of DEP cages in the flow cell.
Hydrodynamic traps allow for the isolation of an individual cell in a "trap" at a single given time by passive microfluidic transport. The number of isolated cells can be manipulated based on the number of traps in the system.
The Laser Capture Microdissection technique utilizes a laser to dissect and separate individual cells, or sections, from tissue samples of interest. The methods involve the observation of a cell under a microscope, so that a section for analysis can be identified and labeled so that the laser can cut the cell. Then, the cell can be extracted for analysis.
Manual single cell picking is a method where cells in a suspension are viewed under a microscope and individually picked using a
micropipette
A pipette (sometimes spelled as pipett) is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. Pipettes come in several designs for various purposes with diffe ...
.
Microfluidics allows for the isolation of individual cells for further analyses. The following principles outline the various microfluidic processes for single-cell separation: droplet-in-oil based isolation, pneumatic membrane valving, and hydrodynamic cell traps. Droplet-in-oil based microfluidics uses oil-filled channels to hold separated aqueous droplets. This allows the single cell to be contained and isolated from the inside the oil based channels. Pneumatic membrane valves use the manipulation of air pressure, to isolate individual cells by membrane deflection. The manipulation of the pressure source allows the opening or closing of channels in a microfluidic network. Typically, the system requires an operator and is limited in throughput.
The technique Raman tweezers combines the use
Raman spectroscopy
Raman spectroscopy () (named after Indian physicist C. V. Raman) is a spectroscopic technique typically used to determine vibrational modes of molecules, although rotational and other low-frequency modes of systems may also be observed. Raman sp ...
and
optical tweezers
Optical tweezers (originally called single-beam gradient force trap) are scientific instruments that use a highly focused laser beam to hold and move microscopic and sub-microscopic objects like atoms, nanoparticles and droplets, in a manner simila ...
, which use a laser beam to trap and manipulate cells.
The development of hydrodynamic-based microfluidic biochips has been increasing over the years. In this technique, the cells are trapped in a particular region for single cell analysis (SCA). This usually occurs without any application of external force fields such as optical, electrical, magnetic or acoustic. There is a need to explore the insights of SCA in the cell's natural state, and development of these techniques is highly essential for that study. Researchers have highlighted the need to develop biochip devices to suit market and researcher demands. Hydrodynamic microfluidics facilitate the development of passive lab-on-chip applications.
Genomics
Techniques
Single-cell genomics is heavily dependent on increasing the copies of DNA found in the cell so there is enough to be sequenced. This has led to the development of strategies for ''whole genome amplification'' (WGA). Currently WGA strategies can be grouped into three categories:
* Controlled priming and PCR Amplification: Adapter-Linker PCR WGA
* Random priming and PCR Amplification: DOP-PCR, MALBAC
* Random priming and isothermal amplification: MDA
The Adapter Linker PCR WGA is reported in many comparative studies to be best performing for diploid single cell mutation analysis, thanks to its very low Allelic Dropout effect, and for copy number variation profiling due to its low noise, both with aCGH and with NGS low Pass Sequencing. This method is only applicable to human cells, both fixed and unfixed.
One widely adopted WGA techniques is called degenerate oligonucleotide–primed polymerase chain reaction (DOP-PCR). This method uses the well established DNA amplification method
PCR to try and amplify the entire genome using a large set of
primers. Although simple, this method has been shown to have very low genome coverage. An improvement on DOP-PCR is
Multiple displacement amplification Multiple displacement amplification (MDA) is a DNA amplification technique. This method can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. The reaction starts by annealing random hexamer primers to the ...
(MDA), which uses random primers and a high fidelity
enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
, usually
Φ29 DNA polymerase
Φ29 DNA polymerase is an enzyme from the bacteriophage Φ29. It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this app ...
, to accomplish the amplification of larger fragments and greater genome coverage than DOP-PCR. Despite these improvement MDA still has a sequence dependent bias (certain parts of the genome are amplified more than others because of their sequence). The method shown to largely avoid the bias seen in DOP-PCR and MDA is
Multiple Annealing and Looping–Based Amplification Cycles (MALBAC). Bias in this system is reduced by only copying off the original DNA strand instead of making copies of copies. The main draw backs to using MALBA, is it has reduced accuracy compared to DOP-PCR and MDA due to the enzyme used to copy the DNA.
Once amplified using any of the above techniques, the DNA can be sequenced using Sanger or
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation s ...
(NGS).
Purpose
There are two major applications to studying the genome at the single cell level. One application is to track the changes that occur in bacterial populations, where phenotypic differences are often seen. These differences are missed by bulk sequencing of a population, but can be observed in single cell sequencing. The second major application is to study the genetic evolution of cancer. Since cancer cells are constantly mutating it is of great interest to see how cancers evolve at the genetic level. These patterns of somatic mutations and copy number aberration can be observed using single cell sequencing.
Transcriptomics
Techniques
Single-cell transcriptomics Single-cell transcriptomics examines the gene expression level of individual cells in a given population by simultaneously measuring the RNA concentration (conventionally only messenger RNA (mRNA)) of hundreds to thousands of genes. Single-cell tra ...
uses sequencing techniques similar to single cell genomics or direct detection using
fluorescence in situ hybridization
Fluorescence ''in situ'' hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence complementarity. It was developed b ...
. The first step in quantifying the transcriptome is to convert RNA to
cDNA
In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA (miRNA)) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to express a speci ...
using
reverse transcriptase
A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, ...
so that the contents of the cell can be sequenced using NGS methods as was done in genomics. Once converted, there is not enough cDNA to be sequenced so the same DNA amplification techniques discussed in single cell genomics are applied to the cDNA to make sequencing possible.
Alternately, fluorescent compounds attached to RNA hybridization probes are used to identify specific sequences and sequential application of different RNA probes will build up a comprehensive transcriptome.
Purpose
The purpose of single cell transcriptomics is to determine what genes are being expressed in each cell. The transcriptome is often used to quantify the gene expression instead of the proteome because of the difficulty currently associated with amplifying protein levels.
There are three major reasons gene expression has been studied using this technique: to study gene dynamics, RNA splicing, and cell typing. Gene dynamics are usually studied to determine what changes in gene expression affect different cell characteristics. For example, this type of transcriptomic analysis has often been used to study embryonic development. RNA splicing studies are focused on understanding the regulation of different
transcript isoforms. Single cell transcriptomics has also been used for cell typing, where the genes expressed in a cell are used to identify types of cells. The main goal in cell typing is to find a way to determine the identity of cells that don't have known
genetic marker A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be ...
s.
Proteomics
Techniques
There are three major approaches to single-cell proteomics: antibody based methods, fluorescent protein based methods, and mass-spectroscopy based methods.
Antibody–based methods
The antibody based methods use designed antibodies to bind to proteins of interest, allowing the relative abundance of multiple individual targets to be identified by one of several different techniques.
''Imaging:'' Antibodies can be bound to fluorescent molecules such as
quantum dot
Quantum dots (QDs) are semiconductor particles a few nanometres in size, having light, optical and electronics, electronic properties that differ from those of larger particles as a result of quantum mechanics. They are a central topic in nanote ...
s or tagged with organic
fluorophore
A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with se ...
s for detection by
fluorescence microscopy
A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. "Fluorescence microsc ...
. Since different colored quantum dots or unique fluorophores are attached to each antibody it is possible to identify multiple different proteins in a single cell. Quantum dots can be washed off of the antibodies without damaging the sample, making it possible to do multiple rounds of protein quantification using this method on the same sample. For the methods based on organic fluorophores, the fluorescent tags are attached by a reversible linkage such as a DNA-hybrid (that can be melted/dissociated under low-salt conditions)
or chemically inactivated,
allowing multiple cycles of analysis, with 3-5 targets quantified per cycle. These approaches have been used for quantifying protein abundance in patient biopsy samples (e.g. cancer) to map variable protein expression in tissues and/or tumors,
and to measure changes in protein expression and cell signaling in response to cancer treatment.
''Mass Cytometry'''':'' rare metal isotopes, not normally found in cells or tissues, can be attached to the individual antibodies and detected by
mass spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is use ...
for simultaneous and sensitive identification of proteins. These techniques can be highly multiplexed for simultaneous quantification of many targets (panels of up to 38 markers) in single cells.
Antibody-DNA quantification: another antibody-based method converts protein levels to DNA levels.
The conversion to DNA makes it possible to amplify protein levels and use NGS to quantify proteins. In one such approach, two antibodies are selected for each protein needed to be quantified. The two antibodies are then modified to have single stranded DNA connected to them that are complementary. When the two antibodies bind to a protein the complementary strands will anneal and produce a double stranded segment of DNA that can then be amplified using PCR. Each pair of antibodies designed for one protein is tagged with a different DNA sequence. The DNA amplified from PCR can then be sequenced, and the protein levels quantified.
Mass spectroscopy–based methods
In mass spectroscopy based proteomics there are three major steps needed for peptide identification: sample preparation, separation of peptides, and identification of peptides. Several groups have focused on oocytes or very early cleavage-stage cells since these cells are unusually large and provide enough material for analysis.
Another approach, single cell proteomics by mass spectrometry (SCoPE-MS) has quantified thousands of proteins in mammalian cells with typical cell sizes (diameter of 10-15 μm) by combining carrier-cells and single-cell barcoding.
The second generation, SCoPE2, increased the throughput by automated and miniaturized sample preparation;
It also improved quantitative reliability and proteome coverage by data-driven optimization of LC-MS/MS and peptide identification. The sensitivity and consistency of these methods have been further improved by prioritization, and massively parallel sample preparation in nanoliter size droplets. Another direction for single-cell protein analysis is based on a scalable framework of multiplexed data-independent acquisition (plexDIA) enables time saving by parallel analysis of both peptide ions and protein samples, thereby realizing multiplicative gains in throughput.
The separation of differently sized proteins can be accomplished by using
capillary electrophoresis
Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other electr ...
(CE) or
liquid chromatography
In chemical analysis, chromatography is a laboratory technique for the Separation process, separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it ...
(LC) (using
liquid chromatography with mass spectroscopy is also known as LC-MS).
This step gives order to the peptides before quantification using
tandem mass-spectroscopy (MS/MS). The major difference between quantification methods is some use labels on the peptides such as
tandem mass tag A tandem mass tag (TMT) is a chemical label that facilitates sample multiplexing in mass spectrometry (MS)-based quantification and identification of biological macromolecules such as proteins, peptides and nucleic acids. TMT belongs to a family of ...
s (TMT) or
dimethyl labels which are used to identify which cell a certain protein came from (proteins coming from each cell have a different label) while others use not labels (quantify cells individually). The mass spectroscopy data is then analyzed by running data through databases that convert the information about peptides identified to quantification of protein levels.
These methods are very similar to those used to
quantify the proteome of bulk cells, with modifications to accommodate the very small sample volume.
= Ionization techniques used in mass spectrometry-based single-cell analysis
=
A huge variety of ionization techniques can be used to analyze single cells. The choice of ionization method is crucial for analyte detection. It can be decisive which type of compounds are ionizable and in which state they appear, e.g., charge and possible fragmentation of the ions. A few examples of ionization are mentioned in the paragraphs below.
Nano-DESI
One of the possible ways to measure the content of single cells is
nano-DESI (nanospray desorption electrospray ionization). Unlike
desorption electrospray ionization
Desorption electrospray ionization (DESI) is an ambient ionization technique that can be coupled to mass spectrometry (MS) for chemical analysis of samples at atmospheric conditions. Coupled ionization sources-MS systems are popular in chemical an ...
, which is a desorption technique, nano-DESI is a liquid extraction technique that enables the sampling of small surfaces, therefore suitable for single-cell analysis. In nano-DESI, two fused silica capillaries are set up in a V-shaped form, closing an angle of approx. 85 degrees. The two capillaries are touching therefore a liquid bridge can be formed between them and enable the sampling of surfaces as small as a single cell. The primary capillary delivers the solvent to the sample surface where the extraction happens and the secondary capillary directs the solvent with extracted molecules to the MS inlet. Nano-DESI mass spectrometry (MS) enables sensitive molecular profiling and quantification of endogenous species as small as a few hundred fmol-s  in single cells in a higher throughput manner. Lanekoff ''et al.'' identified 14 amino acids, 6 metabolites, and several lipid molecules from single cheek cells using nano-DESI MS.
LAESI
In
Laser ablation electrospray ionization
Laser ablation electrospray ionization (LAESI) is an ambient ionization method for mass spectrometry that combines laser ablation from a mid-infrared (mid-IR) laser with a secondary electrospray ionization (ESI) process. The mid-IR laser is used t ...
(LAESI) a laser is used to ablate the surface of the sample and the emitted molecules are ionized in the gas phase by charged droplets from electrospray. Similar to DESI the ionization happens in ambient conditions. Anderton ''et al''. used this ionization technique coupled to a Fourier transform mass spectrometer to analyzed 200 single cells of ''Allium cepa'' (red onion) in high spatial resolution.
SIMS
Secondary ion mass spectrometry
Secondary-ion mass spectrometry (SIMS) is a technique used to analyze the composition of solid surfaces and thin films by sputtering the surface of the specimen with a focused primary ion beam and collecting and analyzing ejected secondary ions. ...
(SIMS) is a technique similar to DESI, but while DESI is an ambient ionization technique, SIMS happens in
vacuum
A vacuum is a space devoid of matter. The word is derived from the Latin adjective ''vacuus'' for "vacant" or "void". An approximation to such vacuum is a region with a gaseous pressure much less than atmospheric pressure. Physicists often dis ...
. The solid sample surface is bombarded by a highly focused beam of primary ions. As they hit the surface, molecules are emitted from the surface and ionized. The choice of primary ions determines the size of the beam and also the extent of ionization and fragmentation. Pareek ''et al.'' performed metabolomics to trace how purines are synthesized within purinosomes and used isotope labeling and SIMS imaging to directly observe hotspots of metabolic activity within frozen HeLa cells.
MALDI
In
matrix-assisted laser desorption and ionization (MALDI), the sample is incorporated in a chemical matrix that is capable of absorbing energy from a laser. Similar to SIMS, ionization happens in vacuum. Laser irradiation ablates the matrix material from the surface and results in charged gas phase matrix particles, the analyte molecules are ionized from this charged chemical matrix. Liu ''et al.'' used MALDI-MS to detect eight phospholipids from single A549 cells.
Purpose
The purpose of studying the proteome is to better understand the activity of cells at the single cells level. Since proteins are responsible for determining how the cell acts, understanding the proteome of single cell gives the best understanding of how a cell operates, and how gene expression changes in a cell due to different environmental stimuli. Although transcriptomics has the same purpose as proteomics it is not as accurate at determining gene expression in cells as it does not take into account
post-transcriptional regulation
Post-transcriptional regulation is the control of gene expression at the RNA level. It occurs once the RNA polymerase has been attached to the gene's promoter and is synthesizing the nucleotide sequence. Therefore, as the name indicates, it occ ...
.
Transcriptomics is still important as studying the difference between RNA levels and protein levels could give insight on which genes are post-transcriptionally regulated.
Metabolomics
Techniques
There are four major methods used to quantify the metabolome of single cells, they are: fluorescence–based detection, fluorescence biosensors,
FRET
A fret is any of the thin strips of material, usually metal wire, inserted laterally at specific positions along the neck or fretboard of a stringed instrument. Frets usually extend across the full width of the neck. On some historical instrume ...
biosensors, and mass spectroscopy. The first three methods listed use fluorescence microscopy to detect molecules in a cell. Usually these assays use small fluorescent tags attached to molecules of interest, however this has been shown be too invasive for single cell metabolomics, and alters the activity of the metabolites. The current solution to this problem is to use fluorescent proteins which will act as metabolite detectors, fluorescing when ever they bind to a metabolite of interest.
Mass spectroscopy is becoming the most frequently used method for single cell metabolomics. Its advantages are that there is no need to develop fluorescent proteins for all molecules of interest, and is capable of detecting metabolites in the
femtomole
The mole, symbol mol, is the unit of amount of substance in the International System of Units (SI). The quantity amount of substance is a measure of how many elementary entities of a given substance are in an object or sample. The mole is defi ...
range.
Similar to the methods discussed in proteomics, there has also been success in combining mass spectroscopy with separation techniques such as capillary electrophoresis to quantify metabolites. This method is also capable of detecting metabolites present in femtomole concentrations.
Another method utilizing capillary microsampling combined with mass spectrometry with ion mobility separation has been demonstrated to enhance the molecular coverage and ion separation for single cell metabolomics.
Researchers are trying to develop a technique that can fulfil what current techniques are lacking: high throughput, higher sensitivity for metabolites that have a lower abundance or that have low ionization efficiencies, good replicability and that allow quantification of metabolites.
Purpose
The purpose of single cell metabolomics is to gain a better understanding at the molecular level of major biological topics such as: cancer, stem cells, aging, as well as the development of drug resistance. In general the focus of metabolomics is mostly on understanding how cells deal with environmental stresses at the molecular level, and to give a more dynamic understanding of cellular functions.
Reconstructing developmental trajectories
Single-cell transcriptomic assays have allowed reconstruction development trajectories. Branching of these trajectories describes cell differentiation. Various methods have been developed for reconstructing branching developmental trajectories from single-cell transcriptomic data.
They use various advanced mathematical concepts from
optimal transportation to principal graphs.
Some software libraries for reconstruction and visualization of lineage differentiation trajectories are freely available online.
[Pinello Lab]
Single-Cell Trajectory Reconstruction Exploration and Mapping
/ref>
Cell–cell interaction
Cell–cell interaction Cell–cell interaction refers to the direct interactions between cell surfaces that play a crucial role in the development and function of multicellular organisms.
These interactions allow cells to communicate with each other in response to changes ...
s are characterized by stable and transient interactions.
See also
* Cell sorting Cell sorting is the process through which a particular cell type is separated from others contained in a sample on the basis of its physical or biological properties, such as size, morphological parameters, viability and both extracellular and intra ...
* Micro-arrays for mass spectrometry
* Single-cell variability
In cell biology, single-cell variability occurs when individual cells in an otherwise similar population differ in shape, size, position in the cell cycle, or molecular-level characteristics. Such differences can be detected using modern single-c ...
References
Further reading
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Analytical chemistry
Biochemistry
Cell biology
Laboratory techniques
Scientific techniques