Public Apps
The links below connect to Shiny App visualizations of our published data sets. They are intended to provided functional access beyond the published and shared datasets allowing users to explore, plot, and/or run analyses of our published datasets. Please contact Richard P. if you have issues connecting to these. Note that some, especially those with larger datasets, may take a few seconds to render.
- ROSMAP – iPSCs
- Contains RNAseq and TMT-Proteomics data from iPSC derived neurons (iN; Ngn2 directed differentiation), and astrocytes (iA; SOX9+NFIB directed differentiation). Explorer allows users to plot expression levels across categorical variables and to correlate them with other measurements.
- SORL1 – multiple cell types
- Bulk RNAseq data for WT (CRISPR control) and SORL1 KO cells including iPSCs, and iPSC derived cells (neurons, microglia, astrocytes, and endothelial “like” cells.
- INPP5D – Microglia RNAseq and Proteomics
- RNAseq and TMT-Proteomics data from iPSC derived microglia (iMGL; modified Blurton-Jones protocol). Samples include INPP5D-KO, INPP5D-HET, WT, and 3AC (INPP5D inhibitor) v. Vehicle treatment.
- POU3F2 and WNT signaling in NPCs
- Bulk and single-cell RNAseq, TMT proteomics, CUT&RUN, and IP-Mass Spec data on neural progenitor cells from both WT and POU3f2 mutant backgrounds.
- iAstrocyte -omics from ROSMAP subjects
- Bulk and single-cell (stimulated and unstimulated) RNAseq as well as TMT-proteomics from iPSC derived astrocytes (SOX9+NFIB protocol). Bulk RNAseq and TMT-MS profile 44 different genetic backgrounds.
TYP Lab internal Apps
The links below connect to Shiny Apps that are for internal lab access only. All completed and peer reviewed data sets will be released to the public domain once fully tested. If you are in the lab and need access to any of the following apps, please email Richard P. and he’ll send you an invite.
- Clusterin (CLU) Modulation of Activation in iPSC Derived Astrocytes
- Quantitation of CLU levels in: ROSMAP brain extracts; CLU WT and KO induced Neurons and Astrocytes; Proteomics of iNs and iMGLs exposed to CLU WT or KO iAstrocytes; scRNAseq of triple cultures (iNs, iAs, iMGLs), and single cultures (iNs, and iMGLs) with WT v. KO analysis.
- ROSMAP SNP Effect Browser
- Genetic analysis of the effects of different disease-relevant SNPs on genome-wide RNA and Protein levels (where available), in induced Neurons, Neural Progenitor Cells, Astrocytes, Microglia .
- Response of BBB model to fAD neurons
- TMT-MS protein levels in Neurons, Astrocytes, Microglia, and Brain Endothelial Cells exposed to WT or familial AD (fAD) neurons.