✎ multiomics_analysis_for_dementia [oncinfo]

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<h2>Objectives</h2>
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<p>
Determine biomarkers for Alzheimer's and other neurodegenerative diseases using comprehensive analysis of various data including genomics, epigenomics, metabolomics, proteomics, etc.
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<h3>Objectives</h3>
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<h2>Data</h2>
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<li class="level1"> Whole RNA-seq on 3 control and 3 tau transgenic samples. Each sample is composed of heads of 6 male and 6 female flies, all 10 days old.</li>
<li class="level1"> Small RNA sequencing on the same above samples.</li>
<li class="level1"> Human RNA-Seq data from Mayo Clinic to test <a href="https://docs.google.com/document/d/1-bSoPTcxmw1dnRxpk2V1k91i4-j6wsAo9d6EoWaBAFE/edit" class="urlextern" title="https://docs.google.com/document/d/1-bSoPTcxmw1dnRxpk2V1k91i4-j6wsAo9d6EoWaBAFE/edit" rel="ugc nofollow">these</a> hypotheses, which Bess made based on Drosophila data. Specifically, the raw fastq files from <a href="https://www.synapse.org/#!Synapse:syn5550404" class="urlextern" title="https://www.synapse.org/#!Synapse:syn5550404" rel="ugc nofollow">MayoRNAseq</a> dataset for NCI, PSP, AD, and PA (Synapse ID: syn5550404, cerebellum and temporal cortex).</li>
<li class="level1"> Human RNA-seq data from iPSC-derived neurons from 3 patients with tauopathy, along with 3 CRISPR-corrected isogenic control samples. On 24 April 2018, Celeste Karch provided us with bam files of the data from their JAMA Neurology 2018 paper (<a href="https://bitbucket.org/habilzare/alzheimer/src/master/data/human/iPSC-derived-neurons_2018-04-24/readme.txt" class="urlextern" title="https://bitbucket.org/habilzare/alzheimer/src/master/data/human/iPSC-derived-neurons_2018-04-24/readme.txt" rel="ugc nofollow">readme.txt</a>).</li>
<li class="level1"> <a href="https://www.cell.com/cell/fulltext/S0092-8674(18)30720-7" class="urlextern" title="https://www.cell.com/cell/fulltext/S0092-8674(18)30720-7" rel="ugc nofollow">Single</a>-cell sequencing data (<a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107451" class="urlextern" title="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107451" rel="ugc nofollow">GSE107451</a>) of Drosophila brain in 2 age groups with a median of 53K reads from 57K cells. They identified 87-151 cell types.</li>
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multiomics_analysis_for_dementia.1539867633.txt.gz · Last modified: 2018/10/18 13:00 by admin

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