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<!DOCTYPE html>
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<title>2 Aims and Objectives | RNA-Sequencing to improve characterisation and production of iPSC-induced cardiomyocytes</title>
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<meta name="twitter:title" content="2 Aims and Objectives | RNA-Sequencing to improve characterisation and production of iPSC-induced cardiomyocytes" />
<meta name="author" content="Harithaa Anandakumar" />
<meta name="date" content="2020-01-01" />
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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#need-for-better-therapeutics"><i class="fa fa-check"></i><b>1.1</b> Need for better therapeutics</a><ul>
<li class="chapter" data-level="1.1.1" data-path="index.html"><a href="index.html#immunological-responses-in-transplantations"><i class="fa fa-check"></i><b>1.1.1</b> Immunological Responses in Transplantations</a></li>
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<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#engineered-human-myocardium"><i class="fa fa-check"></i><b>1.2</b> Engineered Human Myocardium</a><ul>
<li class="chapter" data-level="1.2.1" data-path="index.html"><a href="index.html#cgmp-and-quality-control-of-tissue-engineered-products"><i class="fa fa-check"></i><b>1.2.1</b> cGMP and Quality Control of Tissue Engineered Products</a></li>
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<li class="chapter" data-level="1.3" data-path="index.html"><a href="index.html#rnaseq"><i class="fa fa-check"></i><b>1.3</b> RNA Sequencing</a><ul>
<li class="chapter" data-level="1.3.1" data-path="index.html"><a href="index.html#bulkrna"><i class="fa fa-check"></i><b>1.3.1</b> Single cell versus bulk RNA Seq</a></li>
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<li class="chapter" data-level="1.4" data-path="index.html"><a href="index.html#compdeconv"><i class="fa fa-check"></i><b>1.4</b> Computational deconvolution</a></li>
<li class="chapter" data-level="1.5" data-path="index.html"><a href="index.html#exploratory-data-analysis-in-rna-sequencing"><i class="fa fa-check"></i><b>1.5</b> Exploratory Data Analysis in RNA-Sequencing</a><ul>
<li class="chapter" data-level="1.5.1" data-path="index.html"><a href="index.html#pca"><i class="fa fa-check"></i><b>1.5.1</b> Principal Component Analysis (PCA)</a></li>
</ul></li>
<li class="chapter" data-level="1.6" data-path="index.html"><a href="index.html#rationale"><i class="fa fa-check"></i><b>1.6</b> Rationale for the current work</a></li>
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<li class="chapter" data-level="2" data-path="aims-and-objectives.html"><a href="aims-and-objectives.html"><i class="fa fa-check"></i><b>2</b> Aims and Objectives</a></li>
<li class="chapter" data-level="3" data-path="methods.html"><a href="methods.html"><i class="fa fa-check"></i><b>3</b> Methods</a><ul>
<li class="chapter" data-level="3.1" data-path="methods.html"><a href="methods.html#general-analysis-pipeline-of-bulk-rna-seq-data"><i class="fa fa-check"></i><b>3.1</b> General Analysis Pipeline of Bulk RNA-Seq Data</a></li>
<li class="chapter" data-level="3.2" data-path="methods.html"><a href="methods.html#singleCell"><i class="fa fa-check"></i><b>3.2</b> Single Cell Reference Data and CIBERSORTX</a><ul>
<li class="chapter" data-level="3.2.1" data-path="methods.html"><a href="methods.html#processing-of-single-cell-data"><i class="fa fa-check"></i><b>3.2.1</b> Processing of Single Cell Data</a></li>
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<li class="chapter" data-level="3.3" data-path="methods.html"><a href="methods.html#analysis-of-rhesus-rna-seq"><i class="fa fa-check"></i><b>3.3</b> Analysis of Rhesus RNA-Seq</a></li>
<li class="chapter" data-level="3.4" data-path="methods.html"><a href="methods.html#estBacVir"><i class="fa fa-check"></i><b>3.4</b> Estimating Bacterial and Viral Contaminants</a></li>
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<li class="chapter" data-level="4" data-path="results-and-discussion.html"><a href="results-and-discussion.html"><i class="fa fa-check"></i><b>4</b> Results and Discussion</a><ul>
<li class="chapter" data-level="4.1" data-path="results-and-discussion.html"><a href="results-and-discussion.html#general-workflow-and-mapping-statistics"><i class="fa fa-check"></i><b>4.1</b> General Workflow and Mapping Statistics</a></li>
<li class="chapter" data-level="4.2" data-path="results-and-discussion.html"><a href="results-and-discussion.html#exploring-potential-microbial-contamination-using-rna-seq-data"><i class="fa fa-check"></i><b>4.2</b> Exploring Potential Microbial Contamination using RNA-Seq Data</a></li>
<li class="chapter" data-level="4.3" data-path="results-and-discussion.html"><a href="results-and-discussion.html#global-view-of-the-transcriptomic-data"><i class="fa fa-check"></i><b>4.3</b> Global view of the transcriptomic data</a><ul>
<li class="chapter" data-level="4.3.1" data-path="results-and-discussion.html"><a href="results-and-discussion.html#correlation-amongst-groups"><i class="fa fa-check"></i><b>4.3.1</b> Correlation amongst groups</a></li>
<li class="chapter" data-level="4.3.2" data-path="results-and-discussion.html"><a href="results-and-discussion.html#gene-level-analysis"><i class="fa fa-check"></i><b>4.3.2</b> Gene-level analysis</a></li>
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<li class="chapter" data-level="4.4" data-path="results-and-discussion.html"><a href="results-and-discussion.html#deconvolution-of-bulk-cms-and-ehms-rna-seq-data"><i class="fa fa-check"></i><b>4.4</b> Deconvolution of Bulk CMs and EHMs RNA-Seq Data</a><ul>
<li class="chapter" data-level="4.4.1" data-path="results-and-discussion.html"><a href="results-and-discussion.html#limits-of-deconvolution"><i class="fa fa-check"></i><b>4.4.1</b> Limits of deconvolution</a></li>
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<li class="chapter" data-level="4.5" data-path="results-and-discussion.html"><a href="results-and-discussion.html#basic-characterisation-of-rhesus-cardiomyocytes"><i class="fa fa-check"></i><b>4.5</b> Basic characterisation of Rhesus Cardiomyocytes</a></li>
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<li class="chapter" data-level="5" data-path="conclusion-and-future-work.html"><a href="conclusion-and-future-work.html"><i class="fa fa-check"></i><b>5</b> Conclusion and Future Work</a></li>
<li class="chapter" data-level="" data-path="summary.html"><a href="summary.html"><i class="fa fa-check"></i>Summary</a><ul>
<li class="chapter" data-level="" data-path="summary.html"><a href="summary.html#task-at-hand"><i class="fa fa-check"></i>Task At Hand</a></li>
<li class="chapter" data-level="" data-path="summary.html"><a href="summary.html#work-done"><i class="fa fa-check"></i>Work Done</a></li>
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<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">RNA-Sequencing to improve characterisation and production of iPSC-induced cardiomyocytes</a>
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<div id="aims-and-objectives" class="section level1">
<h1><span class="header-section-number">2</span> Aims and Objectives</h1>
<p>Stem cell and tissue engineering technologies allow for the potential treatment of heart failure with engineered tissue construtcs — the EHMs. We thus explored RNA-Seq data collected at two stages, as CMs and as EHMs, with the following aims and objectives:</p>
<ol style="list-style-type: decimal">
<li><p>To establish a reusable workflow to analyse the sequenced data — from raw FASTQ files to count files.</p></li>
<li><p>To check for the potential of RNA-Seq to identify microbial contamination.</p></li>
<li><p>To explore the data in context of maturity by comparing with adult and fetal samples from publically available datasets.</p></li>
<li><p>To identify the potential sub-populations via digital deconvolution techniques using a relevant scRNA-Seq dataset.</p></li>
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