Access CARD Data and Tools
CARD builds innovative technologies and resources to support Alzheimer’s disease researchers in their data science and research needs. Some resources are hosted by collaborating institutions.
On this page you can find repositories for:
You can also explore research protocols used by CARD’s research programs.
Induced Pluripotent Stem Cell Lines and Plasmid Repositories
The CARD iPSC Neurodegenerative Disease Initiative’s (iNDI) study on human induced pluripotent stem cell lines generated the following repositories:
- iNDI Cell Line Distribution Portal: Access the KOLF2.1J parental and edited mutant lines.
- Plasmid Repository: Access associated plasmids from the study.
Data Repositories and Research Tools
The following data repositories and tools were generated by CARD's Data Science Expert Group.
- Base Edit Predictor: Explore summaries of the iNDI variants and additional potential single base resolution CRISPR edits for neurodegenerative disorder (NDD) related risk factors.
- CRISPRbrain: An open-science data commons for functional genomics screens in edited, differentiated human cell types. CRISPRbrain is a collaboration with the Kampmann Lab at the University of California, San Francisco.
- CRISPRlipid: An open-science data commons for functional lipidomics screens in edited, differentiated human cell types. CRISPRlipid is a collaboration with the Olzmann Lab at the University of California, Berkeley.
- GenoML: A repository for democratized genomics and automated machine-learning workflows.
- Longitudinal Proteomic Profiling: A web app based tool to browse protein expression trajectories during stem cell neuron differentiation, using the KOLF2.1J cell line.
- Stem Cell Data: Access data on KOLF2.1J — a well-performing human induced pluripotent stem cell line — and its gene-edited derivative clones.
The following repositories and tools will be available soon:
- DIVER: A data harmonization tool (currently in prototype) that aims to support access to all available ADRD and NDD data. DIVER is a collaboration with Johns Hopkins University and the University of Mississippi.
- OmicSynth: Access artificial intelligence-driven network models and causal inferences derived from diverse sets of summary statistics in AD/ADRD multiomics. Alpha version to be released early 2023.
- Spectrum: A data harmonization tool that will combine data on Alzheimer’s disease, amyotrophic lateral sclerosis, and Parkinson’s disease. Spectrum is a collaboration with the University of Illinois Urbana-Champaign. This work sees various dementias and neurodegenerative diseases as a continuum, not discrete units, and will allow deeper exploration of shared disease analyses and manifestations.
Explore code repositories used by CARD’s research programs.
- Genetics Code for KOLF2.1J Lines: This includes the:
- iNDI Genetics Directory: Code for the analysis of whole genome and single-cell sequencing and array-based genotyping of the KOLF2.1J parental line, as described in this iNDI study.
- NBA Genotyping Processing Directory: Code for the analysis of array-based genotyping (Illumina Neurobooster array) results from the KOLF2.1J-edited mutant lines.
- GenoTools: Use this suite of scalable tools to process, control, and manage genotype data from the Data Science Expert Group.
- Long-read Sequencing Code: Code for the analysis of Nanopore long-read DNA sequencing. This code is used by CARD’s Long-read Sequencing Project.
- Proteomics Code: Perform several workflows including: protein analysis and quantification, data processing and clustering, differential expression analysis, and downstream functional enrichment analysis.
- Unified Single Cell Sequencing Code: Pipeline to conduct single-cell and multiome analysis from the Data Science Expert Group.
View research protocols used by CARD’s research programs.
- Brain Tissue Extraction Protocol: This protocol is used by the Long-read Sequencing Project.
- Blood Extraction Protocol: This protocol is used by the Long-read Sequencing Project.
- Cell Culture Protocols: These protocols are used by iNDI.