Work Description

Date: 28th May, 2025

Dataset Title: Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules

Dataset Contact: Pavel Banerjee, [email protected]

Dataset Creators:
Name: Pavel Banerjee
Email: [email protected]
Institution: Department of Chemistry, University of Michigan
ORCID: 0000-0002-7968-8105

Name: Sujay Ray
Email:[email protected]
Institutions: Department of Chemistry and Biochemistry, The University of Mississippi, University, MS, USA

Name: Liuhan Dai
Email:[email protected]
Institutions: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

Name: Erin Sandford
Email: [email protected]
Institution: Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA

Name: Tanmay Chatterjee
Email: [email protected]
Institution: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

Name: Shankar Mandal
Email: [email protected]
Institution: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

Name: Javed Siddiqui
Email: [email protected]
Institution: Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA

Name: Muneesh Tewari
Email: [email protected]
Institution: Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA

Name: Nils G. Walter
Email: [email protected]
Institution: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA

Funding: R21 CA225493 (NIH), MIRA R35 GM131922 , the NCI EDRN (grant number U2C CA271854), NCI SPORE program (grant number P50 CA186786)

Keywords: biomarker, fingerprinting, multiplexed detection, digital encoding, single molecule, multiomic, precision medicine

Research Overview:
Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers—microRNAs (miRNAs), mutant DNAs, and proteins—remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for nanoscale molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.

Methodology:
Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE)
Single Molecule Kinetic Fingerprinting
TIRF Microscopy

Files Contained Here:
The folder contains three sub-folders called: Codes, Consent Forms, Manuscript, SI and Article
Codes: It contains two sub-folders called "Chromato Kinetic Multiplex Codes" and " Color Multiplex Codes".
Chromato Kinetic Multiplex Codes: It contains all the codes needed for doing Chromato kinetic multiplexing with relative path (Blue Depository\Codes\Chromato Kinetic Multiplex Codes) and .xlsx files needed to run the code
Color Multiplex Codes: It contains all the codes needed for doing color multiplexing with relative path (Blue Depository\Codes\Color Multiplex Codes) and .xlsx files, .txt file needed to run the code

Consent Forms: It contains all the consent forms related to prostate cancer patients and CRS patients

Manuscript: It contains six subfolders (Figure 1, Figure 2, Figure 3, Figure 4, Figure 5, Figure 6) providing raw trace files for all six figures of the manuscripts.
Figure 1 Folder: It contains the individual datasets .dat file and representative single trace files of all six miRNAs (cel-miR-39, hsa-miR-16, hsa-miR-141, hsa-miR-375, hsa-miR-29, hs-let-7a)
Figure 2 Folder: It contains all the individual datasets, multiplexed datasets and representative single traces of kinetic multiplexing and color multiplexing experiments.
Figure 3 Folder: It contains datasets (.dat file) for the chromato-kinetic multiplexing and single traces for the ratiometric experiement (hsa-miR-16, hsa-miR-141)
Figure 4 Folder: It contains all trace files for the individual datasets, multiplexing datasets, single traces of let-7 family experiments in buffer and HSL tissue.
Figure 5 Folder: It contains sample plots, traces from tissue samples and patient samples experiments.
Figure 6 Folder: It contains trace files from DNA Multiplexing, Protein Multiplexing, Multiomics detection-triplex and serum multiplexing experiments.
SI: It contains nine subfolders (Figure S1, Figure S2, Figure S4, Figure S5, Figure S10, Figure S11, Figure S12, Figure S16, Figure S17) providing raw trace files for Supporting Information.
Figure S1 Folder: It contains miR 16 sample trace files.
Figure S2 Folder: It contains trace files for different external stimuli's such as different FPs, temperature, probe length, probe concentrations.
Figure S4 Folder: It contains trace files for duplex datasets of hsa-miR-141, hsa-miR-375- and their 1:1 mixture.
Figure S5 Folder: It contains trace files for individual duplex datasets between hsa-miR-29, hsa-miR-16 and hsa-let-7a.
Figure S10 Folder: It contains the trace files from ratio-metric experiments (hsa-miR-141, hsa-miR-16)
Figure S11 Folder: It contains the trace files from ratio-metric experiments (hsa-miR-29, hsa-let-7a)
Figure S12 Folder: It contains individual trace files of different let 7 family members (hsa-let-7a, hsa-let-7b, hsa-let-7d)
Figure S16 Folder: It contains the trace files of hsa-miR-21 and hsa-miR-16 of anti-ago captured Healthy serum and CRS Serum samples.
Figure S17 Folder: It contains the trace files of IL-8 and IL-8 of multiplexed detection in Healthy serum and CRS Serum samples.

Article: It contains the ACS NANO submitted article

Use and Access:
This dataset is made available under a Creative Commons Public Domain License (CC0 1.0)

To Cite Data:
Banerjee, P., Ray, S., Dai, L., Sanford, E., Chatterjee, T., Mandal, S., Siddiqui, J., Tewari, M., Walter, N. G. (2025). Chromato-Kinetic Fingerprinting Enables Multiomic Digital Counting of Single Disease Biomarker Molecules [Data Set]. University of Michigan - Deep Blue. (DOI: https://doi.org/10.7302/464s-k176).