final micro array

8/8/2019 Final Micro Array

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MICROARRAY

PRESENTED BY:-ROHIT TOMAR (2025)

EKTA SINGH (2026)NEHA YADAV(2027)


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WHY MICROARRAY?

DNA microarray analysis is a techniquethat scientists use to determine whethergenes are on or off. Microarray analysis

involves breaking open a cell, isolating itsgenetic contents, identifying all the genesthat are turned on in that particular celland generating a list of those genes.


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INTRODUCTION

A microarray is a-chip. It is a 2D array on asolid substrate (usually a glass slide orsilicon thin-film cell) that assays large amounts ofbiological material using high-throughput screeningmethods.

A multiplex assay is a type oflaboratory procedure thatsimultaneously measures multiple analytes (dozens ormore) in a single assay.

It is distinguished from procedures that measure one or afew analytes at a time. Multiplex assays within a given

application area or class of technology can be furtherstratified based on how many analytes can be measuredper assay, where "multiplex" refers to those with thehighest number of analyte measurements per assay
http://en.wikipedia.org/wiki/Lab-on-a-chiphttp://en.wikipedia.org/wiki/Arrayhttp://en.wikipedia.org/wiki/Substrate_(materials_science)http://en.wikipedia.org/wiki/Glass_slidehttp://en.wikipedia.org/wiki/Silicon_thin-film_cellhttp://en.wikipedia.org/wiki/Biological_materialhttp://en.wikipedia.org/wiki/High-throughput_screeninghttp://en.wikipedia.org/wiki/Laboratoryhttp://en.wikipedia.org/wiki/Analytehttp://en.wikipedia.org/wiki/Assayhttp://en.wikipedia.org/wiki/Assayhttp://en.wikipedia.org/wiki/Analytehttp://en.wikipedia.org/wiki/Laboratoryhttp://en.wikipedia.org/wiki/High-throughput_screeninghttp://en.wikipedia.org/wiki/Biological_materialhttp://en.wikipedia.org/wiki/Silicon_thin-film_cellhttp://en.wikipedia.org/wiki/Glass_slidehttp://en.wikipedia.org/wiki/Substrate_(materials_science)http://en.wikipedia.org/wiki/Arrayhttp://en.wikipedia.org/wiki/Lab-on-a-chip


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MICROARRAY IN DETAIL

A DNA microarray is a multiplex technology used inmolecular biology. It consists of an arrayed series of thousandsof microscopic spots ofDNAoligonucleotides, specific DNAsequence, known asprobes (or reporters).

This can be a short section of a gene or other DNA element thatare used to hybridize a cDNA or cRNA sample (called target)

under high-stringency conditions. Probe-target hybridization is usually detected and quantified by

detection offluorophore-, silver-, or chemiluminescence-labeledtargets to determine relative abundance of nucleic acidsequences in the target.

Since an array can contain tens of thousands of probes, amicroarray experiment can accomplish many genetic tests inparallel.
http://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Oligonucleotidehttp://en.wikipedia.org/wiki/Hybridization_probehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Nucleic_acid_hybridizationhttp://en.wikipedia.org/wiki/CDNAhttp://en.wikipedia.org/wiki/Fluorophorehttp://en.wikipedia.org/wiki/Genetic_testhttp://en.wikipedia.org/wiki/Genetic_testhttp://en.wikipedia.org/wiki/Fluorophorehttp://en.wikipedia.org/wiki/CDNAhttp://en.wikipedia.org/wiki/Nucleic_acid_hybridizationhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Hybridization_probehttp://en.wikipedia.org/wiki/Oligonucleotidehttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Multiplex_(assay)


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TECHNIQUE OFMICROARRAY

One type of microarray, the cDNA microarray, contains DNAfrom each open reading frame(ORF) from the organism ofinterest spotted on glass microscope slides.

These probes are used to detect cDNA (complementary DNA),which is DNA synthesized from a mature, fully spliced mRNAtranscript.

A robot spots DNA probes onto a 25 x 75 mm glass slidescoated with poly-lysine (poly-lysine creates a positivelycharged matrix to allow the negatively charged DNA to adhereto the slide).

Each of these spots are about 100-150 microns in diameterand are 200-300 microns apart, allowing approximately

20,000 spots to be easily placed on one slide. Once the array is made, two samples of labeled cDNA

(experiment and control samples,) are pooled together andare hybridized to the probes on the array.


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LABELLING

Common labels for nucleic acids for microarrayexperiments are the fluorescent dyes Cy3 andCy5.

A green laser (523nm) excites Cy3 and emittedenergy is detected by an emission filter thatdetects emitted energy at 557-592nm.

Red lasers (635nm) excite Cy5 and emission isdetected by a filter that detects at 650-690nm.


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EXPRESSION

The scatter plot in the left panel, each pointcorresponds to a single spot on the array, showsthe differences in expression ofeach gene (theratio of drug and no drug, red and green, log10red green) and by how much, given by thelog10(fluorescence intensity).

The scatter plot on the right shows thedifferences in expression ofidentical cell cultures(in this case, yeast).

Since the cultures being compared are identical,there are no considerable differences inexpression between them.


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MICROARRAY DATA FROM TWOEXPERIMENTS


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What is a DNA Microarray?

A DNA micorarray allows scientists to perform anexperiment on thousands of genes at the same time.

Each spot on a microarray contains multiple identicalstrands of DNA.

The DNA sequence on each spot is unique. Each spot represents one gene.Thousands of spots are arrayed in orderly rows and

columnson a solid surface (usually glass).The precise location and sequence of each spot is

recorded in a computer database. Microarrays can be the size of a microscope slide, or

even smaller.


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MICRORNAs

MicroRNAs (miRNAs) are post-transcriptional regulatorsthat bind to complementary sequences in thethree prime untranslated regions (3' UTRs) of targetmessenger RNA transcripts (mRNAs). miRNAs are shortribonucleic acid (RNA) molecules, on average only 22

nucleotides long. The human genome may encode over 1000 miRNAs,

which may target about 60% of mammalian genes andare abundant in many human cell types.

Each miRNA may repress hundreds of mRNAs. MiRNAs

are well conserved in eukaryotic organisms and arethought to be a vital component of genetic regulation.
http://en.wikipedia.org/wiki/Three_prime_untranslated_regionhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Ribonucleic_acidhttp://en.wikipedia.org/wiki/Conserved_sequencehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Eukaryotehttp://en.wikipedia.org/wiki/Conserved_sequencehttp://en.wikipedia.org/wiki/Ribonucleic_acidhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Three_prime_untranslated_region


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Protein microarray

A protein microarray, sometimes referred to as a proteinbinding microarray, provides a multiplex approach toidentify proteinprotein interactions, to identify the substratesof protein kinases, to identify transcription factor protein-activation, or to identify the targets of biologically active smallmolecules.

The array is a piece of glass on which different molecules ofprotein or specific DNA binding sequences (as capture probesfor the proteins) have been affixed at separate locations in anordered manner thus forming a microscopic array.

The most common protein microarray is theantibody microarray, where antibodies are spotted onto theprotein chip and are used as capture molecules to detectproteins from cell lysate solutions.
http://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Kinasehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Antibody_microarrayhttp://en.wikipedia.org/wiki/Lysatehttp://en.wikipedia.org/wiki/Lysatehttp://en.wikipedia.org/wiki/Antibody_microarrayhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Kinasehttp://en.wikipedia.org/wiki/Multiplex_(assay)


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In the tissue microarray technique, a hollow needle is used toremove tissue cores as small as 0.6 mm in diameter fromregions of interest in paraffin-embedded tissues such asclinical biopsies or tumor samples.

These tissue cores are then inserted in a recipient paraffinblock in a precisely spaced, array pattern. Sections from this

block are cut using a microtome, mounted on a microscopeslide and then analyzed by any method of standardhistological analysis.

Each microarray block can be cut into 100 500 sections,which can be subjected to independent tests. Tests commonlyemployed in tissue microarray include immunohistochemistry,and fluorescent in situ hybridization. Tissue microarrays areparticularly useful in analysis ofcancer samples.

TISSUE MICROARRAY
http://en.wikipedia.org/wiki/Biopsieshttp://en.wikipedia.org/wiki/Tumorhttp://en.wikipedia.org/wiki/Histological_sectionhttp://en.wikipedia.org/wiki/Microtomehttp://en.wikipedia.org/wiki/Immunohistochemistryhttp://en.wikipedia.org/wiki/Fluorescent_in_situ_hybridizationhttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Fluorescent_in_situ_hybridizationhttp://en.wikipedia.org/wiki/Immunohistochemistryhttp://en.wikipedia.org/wiki/Microtomehttp://en.wikipedia.org/wiki/Histological_sectionhttp://en.wikipedia.org/wiki/Tumorhttp://en.wikipedia.org/wiki/Biopsies


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CELLULAR MICROARRAY

A cellular microarray, is a laboratory tool that allows

for the multiplex interrogation of living cells on thesurface of a solid support.

The support, sometimes called a "chip", is spotted with

varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to theircapture on specific spots. Combinations of differentmaterials can be spotted in a given area, allowing notonly cellular capture, when a specific interaction exists,but also the triggering of a cellular response, change in

phenotype, or detection of a response from the cell. An example of cellular microarrays are

PMHC Cellular Microarrays.
http://en.wikipedia.org/wiki/Laboratoryhttp://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Antibodieshttp://en.wikipedia.org/wiki/Proteinshttp://en.wikipedia.org/wiki/Lipidshttp://en.wikipedia.org/wiki/Phenotypehttp://en.wikipedia.org/wiki/PMHC_Cellular_Microarrayshttp://en.wikipedia.org/wiki/PMHC_Cellular_Microarrayshttp://en.wikipedia.org/wiki/Phenotypehttp://en.wikipedia.org/wiki/Lipidshttp://en.wikipedia.org/wiki/Proteinshttp://en.wikipedia.org/wiki/Antibodieshttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Laboratory


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APPLICATION

Molecular barcoding - Each probe on these arraysis a unique sequence or barcode that allows theidentification of different strains or species presentin a complex population.

Protein arrays - Instead of DNA, these arrays containdifferent proteins on each spot.

These allow the identification of protein-proteininteractions, which are important in many biologicalprocesses.

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