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<h1p>Transcriptomics class for UNIST 2015<span style="font-size: medium;"/p>Definition </spanp>1. What is transcriptomics?</h1p> <p>&nbsp;The study of&nbsp;<span style="color: rgb(37em>transcriptomics</em>, 37also referred to as expression profiling, 37)&nbsp; fontexamines the expression level of mRNAs in a given cell population, often using high-family: sans-serifthroughput techniques based on DNA microarray&nbsp; font-size: 14pxtechnology.&nbsp; line-height: 22px;"</p> <p>The&nbsp;2. Relationship between genomics and transcriptomics</spanp> <b style="color: rgb(37p>Genomics is the study of genomes, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">transcriptomethet total genes in cell or organisms.</bp> <span style="color: rgb(37p>Transcriptomcs is the study of transcriptomes, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is the set of all messenger RNA molecules, includingin one cell or a population of cells.&nbsp;</spanp> <p>I think genomics is a href="http://enlarger field or study than transcriptomics.wikipediaThis is because the transcriptomes are based on gene.org</wikip> <p>3. What are mRNAs?</Messenger_RNA" title="Messenger p> <p>&nbsp;This is called messenger RNA" style="text-decoration: none.&nbsp; color: rgb(11, 0, 128)&nbsp; background-image: none; font-mRNA is a large family: sans-serifof RNA&nbsp; font-size: 14pxmolecules that convey genetic information&nbsp; line-height: 22pxfrom DNA to the ribosome,&nbsp;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,where they specify the amino acid&nbsp;</span><a href="http://ensequence of the protein&nbsp;products of gene expression.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: noneFollowing transcription of primary transcript&nbsp; color: rgbmRNA (11known as pre mRNA)&nbsp;by RNA polymerase, 0processed, 128); background-image: none; font-family: sans-serifmature mRNA is translated&nbsp; font-size: 14px; line-heightinto a polymer of amino acids: 22px;">rRNA</a><span style="color: rgb(37protein, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;as summarized in the central dogma of molecular biology.</spanp> <p>4. How to measure RNA expression?<a href="http:/p> <p>&nbsp;</enp> <p>5.wikipediaRelationship between Transcriptome and Proteome.org</wikip> <p>6. What is a UTR?</Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22pxp> <p>7. What is ncRNA&nbsp;">tRNA?</ap> <span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, and otherp>8. What is poly A&nbsp;?</spanp> <p>&nbsp;<a href="http:/p> <p>&nbsp;</en.wikipedia.org/wiki/Non-coding_RNAp> <p>What to do:</p> <p>1. Apply&nbsp;<a href="http://biolecture.org/index.php/Biology_learning_procedure" title="Non-coding RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;Biology learning procedure">non-coding RNABiology learning procedure</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"/p> <p>&nbsp;</spanp> <a href=p>&nbsp;</p> <p>Reference</p> <p><a href="http://enwww.wikipediabiomedcentral.orgcom/1471-2164/wiki13/Transcription_(genetics)473" title="Transcription (genetics)" style="text-decoration>http: none; color: rgb(11, 0, 128); background//www.biomedcentral.com/1471-image: none; font-family2164/13/473</a></p> <p>https: sans//www.youtube.com/watch?v=UYJfM2-serifY7y8 &nbsp; font-size: 14px; line-height: 22px;">transcribed(Youtube by Illumina Gary Schroth)</ap> <span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;"p>&nbsp;in one cell or a population of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Cell_(biology)" title="Cell (biology)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">cells</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span></p><h1><span style="font-size: medium;">classification of RNA molecule</span></h1><h2><font size="3"><span style="font-size: medium;">mRNA</span></font></h2><p><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Messenger RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a large family of&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;molecules that convey&nbsp;</span><a href="http://en.wikipedia.org/wiki/Genetic_information" title="Genetic information" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">genetic information</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;from&nbsp;</span><a href="http://en.wikipedia.org/wiki/DNA" title="DNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;to the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Ribosome" title="Ribosome" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosome</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, where they specify the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Amino_acid" title="Amino acid" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">amino acid</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">sequence of the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;products of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Gene_expression" title="Gene expression" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">gene expression</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. Following&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transcription</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;of&nbsp;</span><a href="http://en.wikipedia.org/wiki/Primary_transcript" title="Primary transcript" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">primary transcript</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;mRNA (known as&nbsp;</span><a href="http://en.wikipedia.org/wiki/Precursor_mRNA" title="Precursor mRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">pre-mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) by&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA_polymerase" title="RNA polymerase" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA polymerase</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, processed, mature mRNA is&nbsp;</span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;into a polymer of amino acids</span></p><h3 style="margin-left: 40px;"><span style="font-size: medium;">UTR</span></h3><p style="margin-left: 40px;"><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">In&nbsp;</span><a href="http://en.wikipedia.org/wiki/Molecular_genetics" title="Molecular genetics" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">molecular genetics</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">, an&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">untranslated region</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">UTR</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) refers to either of two sections, one on each side of a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Coding_sequence" title="Coding sequence" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">coding sequence</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;on a strand of&nbsp;</span><a href="http://en.wikipedia.org/wiki/MRNA" title="MRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">mRNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">. If it is found on the 5' side, it is called the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Five_prime_untranslated_region" title="Five prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">5' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">leader sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">), or if it is found on the 3' side, it is called the&nbsp;</span><a href="http://en.wikipedia.org/wiki/Three_prime_untranslated_region" title="Three prime untranslated region" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">3' UTR</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(or&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">trailer sequence</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">).</span></p><h3 style="margin-left: 40px;"><span style="font-size: medium;">poly A</span></h3><p style="margin-left: 40px;"><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Polyadenylation</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is the addition of a&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">poly(A) tail</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;to a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Messenger" title="Messenger" class="mw-disambig" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">messenger</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded.</span></p><h2><span style="font-size: medium;">ncRNA</span></h2><p><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">A&nbsp;</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">non-coding RNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(</span><b style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">ncRNA</b><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">) is a functional&nbsp;</span><a href="http://en.wikipedia.org/wiki/RNA" title="RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;molecule that is not&nbsp;</span><a href="http://en.wikipedia.org/wiki/Translation_(genetics)" title="Translation (genetics)" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">translated</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;into a&nbsp;</span><a href="http://en.wikipedia.org/wiki/Protein" title="Protein" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">protein</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">.&nbsp;</span><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">Non-coding RNA genes include highly abundant and functionally important RNAs such as&nbsp;</span><a href="http://en.wikipedia.org/wiki/Transfer_RNA" title="Transfer RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">transfer RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;(tRNAs) and&nbsp;</span><a href="http://en.wikipedia.org/wiki/Ribosomal_RNA" title="Ribosomal RNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">ribosomal RNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">(rRNAs), as well as RNAs such as&nbsp;</span><a href="http://en.wikipedia.org/wiki/MicroRNA" title="MicroRNA" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">microRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;</span><a href="http://en.wikipedia.org/wiki/SiRNA" title="SiRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">siRNAs</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">,&nbsp;and&nbsp;</span><a href="http://en.wikipedia.org/wiki/SnRNA" title="SnRNA" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">snRNAs</a>.</p><h1><span style="font-size: medium;">measurment of RNA expression</span></h1><p><a href="http://en.wikipedia.org/wiki/RNA-seq" title="RNA-seq" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">RNA-seq</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of&nbsp;</span><a href="http://en.wikipedia.org/wiki/DNA_microarray" title="DNA microarray" style="text-decoration: none; color: rgb(11, 0, 128); background-image: none; font-family: sans-serif; font-size: 14px; line-height: 22px;">DNA microarrays</a><span style="color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px; line-height: 22px;">&nbsp;is still used.</span></p><h1><span style="font-size: medium;">Relationship among genome, transcriptome, and proteome</span></h1><p><img src="/ckfinder/userfiles/images/nature06802-f2_2.jpg" width="800" height="335" alt="" /></p>