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- The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of samples. | - The Mount Sinai Brain Bank ([[https://www.synapse.org/#!Synapse:syn3159438|MSBB]]) includes proteome and gene expression profiles from hundreds of samples. |
- The [[https://www.synapse.org/#!Synapse:syn5550404|MayoRNAseq]] includes WGS and RNA-Seq data from 275 Cerebellum (CBE) and 276 Temporal cortex (TCX) samples. | - The [[https://www.synapse.org/#!Synapse:syn5550404|MayoRNAseq]] includes WGS and RNA-Seq data from 275 Cerebellum (CBE) and 276 Temporal cortex (TCX) samples. |
- The Religious Orders Study and Memory and Aging Project ([[https://www.synapse.org/#!Synapse:syn3219045|ROSMAP]]) is the **richest** dataset in AMP-AD in terms of variety of data types, which include gene expression, genome, proteome, metabolome, and image data. Also, DNA methylation, miRNA, WGS, WES, and even H3K9Ac are available for ~1K samples. The dataset is very well [[https://www.radc.rush.edu/docs/omics.htm|documented]]. | - The Religious Orders Study and Memory and Aging Project ([[https://www.synapse.org/#!Synapse:syn3219045|ROSMAP]]) is the **richest** dataset in AMP-AD in terms of variety of data types, which include gene expression, genome, proteome, metabolome, and image data. Also, DNA methylation, miRNA, WGS, WES, and even H3K9Ac are available for ~1K samples. The dataset is very well [[https://www.radc.rush.edu/docs/omics.htm|documented]], and was used to identify [[http://mostafavilab.stat.ubc.ca/xqtl/|xQTL]] by Philip De Jager. |
| - Mathys, Hansruedi, et al. "**Single-cell** transcriptomic analysis of Alzheimer’s disease." Nature ([[https://www.nature.com/articles/s41586-019-1195-2|2019]]). \\ Radek's summary: "Showing ~80K single cell transcriptomic analysis on brain tissues from ~50 patients with Alzheimer's disease. Subpopulations of glia and neurons expressed different gene signatures associated with AD. These enormous cataloging data may help to further pinpoint pathways associated with AD.", and his [[plan|]]. Habil's [[https://docs.google.com/presentation/d/1u2rv9FExW44JfJsqPjenJcCsCFnOSUbJUxQwalviNHk/edit#slide=id.p|presentation]] in Biggs journal club on 2 July 2019. |
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===== Collaborators ===== | ===== Collaborators ===== |
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Dr. [[http://gsbs.uthscsa.edu/faculty/sudha-seshadri-m.d.-dm|Sudha Seshadri]], the Founding Director of The Glenn [[https://biggsinstitute.org/|Biggs Institute]] for Alzheimer's & Neurodegenerative Diseases, and [[https://biggsinstitute.org/team-member/claudia-l-satizabal-phd/|Dr. Claudia Satizabal]]. | Dr. [[http://gsbs.uthscsa.edu/faculty/sudha-seshadri-m.d.-dm|Sudha Seshadri]], the Founding Director of The Glenn [[https://biggsinstitute.org/|Biggs Institute]] for Alzheimer's & Neurodegenerative Diseases, [[https://biggsinstitute.org/team-member/claudia-l-satizabal-phd/|Dr. Claudia Satizabal]], and Dr. [[http://runewarkbiology.rutgers.edu/Dobrowolski Lab/index.html|Radek Dobrowolski]]. |
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===== Subprojects ===== | ===== Subprojects ===== |
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- An interactive **timeline** of Alzheimer's disease by [[https://www.alzforum.org/timeline/alzheimers-disease#2010|AlzForum]]. | - An interactive **timeline** of Alzheimer's disease by [[https://www.alzforum.org/timeline/alzheimers-disease#2010|AlzForum]]. |
- Mathys, Hansruedi, et al. "**Single-cell** transcriptomic analysis of Alzheimer’s disease." Nature ([[https://www.nature.com/articles/s41586-019-1195-2|2019]]). \\ Radek's summary: "Showing single cell transcriptomic analysis on brain tissues from ~50 patients with Alzheimer's disease. Subpopulations of glia and neurons expressed different gene signatures associated with AD. These enormous cataloging data may help to further pinpoint pathways associated with AD.", and his {{:wiki:img_20190516_162440263.jpg?linkonly|plan}}. | |
- Satizabal, Claudia L., et al. "Genetic architecture of subcortical brain structures in over 40,000 individuals worldwide." [[https://www.biorxiv.org/content/10.1101/173831v1.full|bioRxiv]] (2017): 173831. \\ They identified a set of genes that is "significantly enriched for //Drosophila// orthologs associated with neurodevelopmental phenotypes". | - Satizabal, Claudia L., et al. "Genetic architecture of subcortical brain structures in over 40,000 individuals worldwide." [[https://www.biorxiv.org/content/10.1101/173831v1.full|bioRxiv]] (2017): 173831. \\ They identified a set of genes that is "significantly enriched for //Drosophila// orthologs associated with neurodevelopmental phenotypes". |
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