Computing @ NSCI
At NSCI our work relies on computational resources. Large datasets and uniquely structured experimental methods require novel interpretations of typical informatic techniques. Close collaboration between computational and experimental scientists ensures the value of our contributions. Below find links to our interactive data sets as well as publicly available data for download.
Public Data Sets
Cortecon: RNA-seq data collected during corticogenesis. Browse this data at http://cortecon.neuralsci.org , Citation: CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development From Human Embryonic Stem Cells. van de Leemput et. al, Neuron (2014), view the paper online at Neuron.
RPE/EMT: Chip-seq Data collected to characterize the epithelial-mesenchymal transition in retinal pigment epithelium. There are four components to this data
- Explore Networks RPE up
- Explore Networks EMT up
- View EMT motifs
- View RPE motifs
- TP53 networks
- LFS networks
RPE & Nicotinamide: RNA-seq analysis to examine the global impact of Nicotinamide (NAM) on hiPSC-derived RPE transcriptome in order to better understand the mechanism of action of NAM. NAM inhibited the expression of Age related Macular degeneration (AMD) associated protein transcripts in hiPSC-derived RPE.
- Read the paper: https://doi.org/10.1016/j.stem.2016.12.015
- Download from the Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90889
Aging in the the Subventricular Zone: Expression profiling by high throughput sequencing of RNA extracted from Mouse SVZ, in triplicate, from ages 2, 6, 18 and 22 months.
- Read the paper: https://doi.org/10.1016/j.stemcr.2017.10.005
- Download the data from the Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104651