Mount Sinai Institute for Systems Biomedicine

Resources

Researchers in the Institute have developed both experimental and computational resources that enable genome wide systems analyses. These resources have been developed with support from National Institute of Health (NIH) Center grants and are freely available to the academic research community.  Several of these resources are available from NIH consortia websites.

Healthy Human Stem Cell Library

Mount Sinai Healthy Human Induced Pluripotent Stem Cell Resource

We have generated a library of human induced pluripotent stem cells (hiPSCs) from clinically well-characterized, diverse healthy human individuals. The library consists of hiPSCs reprogrammed using non-integrating methods from dermal skin fibroblasts of forty consented individuals (22 men and 18 women ranging in age from twenty-two to sixty-one years). These individuals were selected by a three-physician panel after having passed of a rigorous health screen. Generated hiPSCs were thoroughly characterized for having a normal karyotype, matching to the respective parental fibroblasts through short-tandem repeat analysis (authentication; available under restricted control access at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002088.v2.p1#), expression of pluripotency markers by immunocytochemistry, and having a mRNA-sequencing-based transcriptional profile characteristic of pluripotent stem cells (PluriTest® analysis). Further characterization included whole genome sequencing (available under restricted control access at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002088.v2.p1#), ancestry determination, enhanced carrier screen, and Mendelian disease genes and risk analysis.  This resource was developed as part of the LINCS Center grant funded by the NIH Common Fund.

Availability from the Stem Cell Engineering Core

Currently, three male and three female hiPSC lines (MSN02-01S, MSN04-05S, MSN09-02S, MSN25-09S, MSN38-04S and MSN39-04S) can be obtained by Mount Sinai Researchers through the Mount Sinai Stem Cell Engineering CoRE (https://icahn.mssm.edu/research/portal/resources/deans-cores/stem-cell-engineering; contact Samuele Marro, PhD at samuele.marro@mssm.edu

Availability from the Institute of Systems Biomedicine

12 male and 12 female hiPSC lines (MSN01-02S, MSN02-01S, MSN04-05S, MSN05-01R, MSN06-07R, MSN07-07S, MSN08-06S, MSN09-02S, MSN10-01R, MSN11-05S, MSN12-04S, MSN13-03S, MSN14-01S, MSN15-31S, MSN17-07S, MSN19-07S, MSN20-06S, MSN23-01S, MSN25-09S, MSN27-03S, MSN29-03S, MSN30-01S, MSN38-c4S) are available by contacting Srinivas Ravi Iyenga, PhD (ravi.iyengar@mssm.edu) or Christoph Schaniel, PhD (Christoph.schaniel@mssm.edu)

A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals

Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Rafael Dariolli, Sunita L. D’Souza, Arjun S. Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth I. Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen S. Lynch, Katherine C. Michelis, Neelima C. Tangirala, Himali Weerahandi, David C. Thomas, Kristin G. Beaumont, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C. Schürer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar

A Library of Induced Pluripotent Stem Cells from Clinically Well-Characterized, Diverse Healthy Human Individuals 

bioRxiv 2020.10.29.360909; doi: https://doi.org/10.1101/2020.10.29.360909

The Kidney Precision Medicine Project Reference Atlas

The Kidney Precision Medicine Project (KPMP) is a multi-project consortium funded by the National Institute of Diabetes and Digestive and Kidney Diseases to develop multiscale understanding of the human kidney and finding new therapies for kidney disease.  One focus of the project is the development of a kidney atlas at single cell resolution that maps healthy and diseased states. Institute researchers Evren U. Azeloglu, PhD, Jens Hansen, PhD, Yongqun He, PhD, Srinivas Iyengar, PhD and Yuguang Xiong are part of the KPMP consortium and developed the bioinformatics models for the construction of the kidney reference tissue atlas.

A manuscript describing Bioinformatic Integration of the data is available at BioRxiv

Jens Hansen, Rachel Sealfon, Rajasree Menon, Michael T. Eadon, Blue B. Lake, Becky Steck, Dejan Dobi, Samir Parikh, Tara K. Sigdel, Guanshi Zhang, Dusan Velickovic, Daria Barwinska, Theodore Alexandrov, Priyanka Rashmi, Edgar A. Otto, Michael P. Rose, Christopher R. Anderton, John P. Shapiro, Annapurna Pamreddy, Seth Winfree, Yongqun He, Ian H. de Boer, Jeffrey B. Hodgin, Laura Barisoni, Abhijit S. Naik, Kumar Sharma, Minnie M. Sarwal, Kun Zhang, Jonathan Himmelfarb, Brad Rovin, Tarek M. El-Achkar, Zoltan Laszik, John Cijiang He, Pierre C. Dagher, M. Todd Valerius, Sanjay Jain, Lisa Satlin,Olga G. Troyanskaya, Matthias Kretzler, Ravi Iyengar, Evren U. Azeloglu, for the Kidney Precision Medicine Project.

A reference tissue atlas for the human kidney.  bioRxiv 2020.07.23.216507; doi: https://doi.org/10.1101/2020.07.23.216507

View the data, which is available for further analysis

Systems Biology Massive Open Online Courses

The Systems Biology Specialization in Coursera covers the concepts and methodologies used in systems-level analysis of biomedical systems. Several Institute investigators teach the five course series. Successful participants will learn how to use experimental, computational and mathematical methods in systems biology and how to design practical systems-level frameworks to address questions in a variety of biomedical fields. In the final Capstone Project, students will apply the methods they learned in five courses of specialization to work on a research project.

Find further details and free course enrollment