Datasets and resources

Page Summary

Over the past two decades of our research in islet biology, we have been fortunate to collaborate and connect with several surgeons, researchers and data scientists who have helped us through contribution, assessment and analysis of several hundreds of human tissues/samples, which are consented for research. We acknowledge the support from our funders, surgical teams and associated staff and most importantly the consenting relatives/donors for the cell/tissue samples received. We provide a dataset of human islets, pancreas, gallbladders, brains, spleen, endothelium, smooth muscle, and other human tissues that we have (and continue to) profile using bulk RNA seq, microRNA discovery and mRNA profiling/validation approaches. We also continue to gather and build metadata related to these samplesets and analyse these through scRNA-seq/profiling technologies. We believe that bigger and better goals could be achieved through healthy collaborative research. We are happy to join hands with like-minded researchers, sharing interests in analysing the expression of mRNAs and ncRNAs in insulin-transcribing human tissues as well as other tissues not known to transcribe the human (pro-)insulin gene. We look forward to discussing opportunities towards building strengths through such collaborative research networks.

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Datasets interested in
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GSE152419

Contributors: Mugdha Joglekar, Wilson Wong, David Martin, Anandwardhan Hardikar This dataset contains bulk RNA seq data from human gallbladder epithelial cell preparations. We also have a larger (and overlapping) dataset of human gallbladder discovery microRNA profiles from these and other gallbladder epithelial cell samples. The same GEO dataset contains bulk RNA-seq data from adult mouse gallbladder and pancreas. Human gallbladder data available through our lab includes:
  • microRNA profiles;
  • Insulin content and some functional data in mice;
  • Clinical history/diabetes status, insulin copy number (ddPCR), frozen cell culture samples and dry pellets.

GSE152111

Contributors: Wilson Wong, Mugdha Joglekar, Yi Vee Chew, Wayne J Hawthorne and Anandwardhan Hardikar This dataset contains bulk RNA seq data (~35-40 Million clean reads) from n=66 human cadaveric islet donor preparations with overlapping microRNA data for most of these donors. Data available through collaboration related to such preparations includes:
  • Donor characteristics and islet isolation parameters;
  • Insulin content and functional data;
  • microRNA profiles;
  • Clinical history, diabetes status, insulin copy number (ddPCR), islet-derived cell populations (hIPCs) and frozen dry pellets for some.

GSE134068

Contributors: Wilson Wong, Mugdha Joglekar, Yi Vee Chew, Wayne Hawthorne and Anandwardhan Hardikar This dataset contains high depth (~90 Million clean reads/sample) bulk RNA seq data from n=18 human islet preparations stratified on the basis of their post-isolation islet quality. We also have data for high density discovery microRNAs using TaqMan-based real-time quantitative PCR. Data available through collaboration related to these preparations include:
  • Donor characteristics and islet isolation parameters;
  • Insulin content and functional data;
  • microRNA profiles;
  • Clinical history, diabetes status, insulin copy number (ddPCR) and frozen dry pellets for some.

miRNA and ddPCR datasets

Key contributors (data aquisition/analysis): Wilson Wong, Mugdha Joglekar, Charlotte Dong, Sarang Satoor, Ryan Farr, Cody-Lee Maynard, Michael Williams and Anandwardhan Hardikar1) Bulk RNA and scRNA-seq datasets from our other (unpublished) sequencing preparations of human adipose, gallbladder, brain, islet-derived progenitor cells and comparisons to other public datasets of human pancreatic islet cells preparations. 2) A custom microRNA and insulin cfDNA profile of islet beta-cell death from ethnically diverse sets of plasma samples (n~3000) from individuals without or with type 1 diabetes. 3) Discovery microRNA profiles of human tissues from over 400 human tissues including pancreas (ND and T2D), islets (ND and T2D), gallbladders, brains, endothelium, smooth muscle, spleen and other tissues.

Data analytical tools

The Hardikar Lab is involved in analysing data from large transcriptomic datasets involving microRNA, lncRNA and mRNA profiles from several hundreds to thousands of cell/tissue/plasma samples. The lab staff/students have training, experience and expertise in multiple analytical workflows involving:
  • high density real-time qPCR analysis;
  • univariate and multivariate biostatistical analysis;
  • machine-learning analytical workflows;
  • single cell (sc) RNA sequencing;
  • pseudotime analysis and data visualization;
  • bulkRNA-seq analysis (STRAND LS);
  • Pathway analysis (Ingenuity, Panther etc..).