Genomic Technology Development

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Project Title Project Number Contact PI / Project Leader Organization Name Publications TDCC Status
Ultra low-input epigenetic sequencing with combined enzymatic and long-read technologies HG010646 KOHLI, RAHUL MANU (contact); FANG, GANG UNIVERSITY OF PENNSYLVANIA View publication Active
NextGen Spatial Multi-omics Technologies HG014032 VICKOVIC, SANJA NEW YORK GENOME CENTER View publication Active
Computational and experimental approaches to decode domain-specific protein-RNA interactions HG014077 ZHANG, CHAOLIN (contact); WANG, LEI COLUMBIA UNIVERSITY View publication Active
Functional RNA elements in the human genome HG004659 YEO, EUGENE WEI-MING (contact); CORBETT, KEVIN DANIEL UNIVERSITY OF CALIFORNIA, SAN DIEGO View publication Active
Preparation of sequencing libraries for multi-analyte analysis of RNAs HG013284 KAZAKOV, SERGEI A REALSEQ BIOSCIENCES, INC. View publication Active
Transcriptomic characterization of membraneless organelles with scalable resolution HG013495 FEI, JINGYI UNIVERSITY OF CHICAGO View publication Active
Self-Evolvr: self-refreshing molecular barcodes using CRISPR-self-guided mutagenesis HG014016 BAYM, MICHAEL HARVARD MEDICAL SCHOOL View publication Active
CRISPR-based depletion method for resolving pseudogene contamination in Next Generation Sequencing (NGS) based genetic testing HG014080 BROWN, KEITH JUMPCODE GENOMICS View publication Active
A multimodal MPRA platform to study regulatory sequence function HG014094 HEINZ, SVEN W (contact); BENNER, CHRISTOPHER W UNIVERSITY OF CALIFORNIA, SAN DIEGO View publication Active
Multiplexed Locus-Specific Hypermutation for Functional Characterization of the Coding and Noncoding Genome HG013336 CHEN, FEI BROAD INSTITUTE, INC. View publication Active
Pioneering assays for spatially-resolved single-cell multiomics HG013294 HARTOULAROS, GEORGE SURVEY GENOMICS, INC. View publication Active
Smart Laser Capturing Microscope for Genome Wide Single Cell Spatial Transcriptomics HG014004 CANG, HU (contact); SUN, SHA UNIVERSITY OF CALIFORNIA-IRVINE View publication Active
Expansion genomics for high-resolution single-cell and spatial epigenomics HG013679 BUENROSTRO, JASON DANIEL HARVARD UNIVERSITY View publication Active
Developing next-generation high-content image-based genetic screens for multi-omic spatial phenotypes HG013503 WANG, SIYUAN YALE UNIVERSITY View publication Active
Scalable and quantitative chromatin profiling from formalin-fixed paraffin-embedded samples HG013071 KEOGH, MICHAEL-CHRISTOPHER EPICYPHER, INC. View publication Active
Mechanisms of Chromosome Fragile Site Formation in the Human Genome HG012629 FENG, WENYI UPSTATE MEDICAL UNIVERSITY View publication Active
Commercialization of a rapid, automated Hi-C platform for sensitive genomic profiling of multiple cancer sample types HG014126 MUNDING, LISA CANTATA BIO LLC View publication Active
A platform for scalable spatial single cell genomics HG010647 CHEN, FEI (contact); MACOSKO, EVAN Z BROAD INSTITUTE, INC. View publication Active
High-throughput biochemistry with RNA-barcoded proteins HG013504 FIELDS, STANLEY (contact); QUEITSCH, CHRISTINE UNIVERSITY OF WASHINGTON View publication Active
Genome-wide assessment of transcriptional state history HG013472 BREUSS, MARTIN WERNER UNIVERSITY OF COLORADO DENVER View publication Active
Whole organ transcriptome reconstruction by dimensionality reduced fluorescent in situ hybridization HG012925 WOLLMAN, ROY (contact); LI, JINGYI JESSICA UNIVERSITY OF CALIFORNIA LOS ANGELES View publication Active
Multimodal Analysis of the Genome Architecture Using Expansion Microscopy HG012969 GIRALDEZ, ANTONIO J (contact); BEWERSDORF, JOERG ; WANG, SIYUAN YALE UNIVERSITY View publication Active
Spatially Resolved Molecular Measurement of Biomolecular Condensates HG013358 CHEN, HAIQI UT SOUTHWESTERN MEDICAL CENTER View publication Active
DNA-optical barcoding technology for spatiotemporal single-cell analysis HG013591 KWOK, SHELDON J J LASE INNOVATION INC. View publication Active
A novel flexible approach for high-throughput single-cell phenotyping and genotyping HG013448 SOUMILLON, MAGALI FLEXOMICS LLC View publication Active
Influences of DNA sequence and histone features on transcription factor binding to nucleosomes HG012246 BULYK, MARTHA L BRIGHAM AND WOMEN'S HOSPITAL View publication Active
MutSensor System: A Set of Highly Sensitive Mutation Reporters to Dissect Genome Stability in Health and Disease HG012590 DAVOLI, TERESA (contact); BOEKE, JEF D; NEW YORK UNIVERSITY SCHOOL OF MEDICINE View publication Active
Development of multi-color 3D super-localization LiveFISH and LiveFISH PAINT to investigate the chromatin dynamics at any genomic scale HG013133 QI, LEI STANLEY STANFORD UNIVERSITY View publication Active
Decoding global RNP topologies in splicing regulation HG012928 LU, ZHIPENG UNIVERSITY OF SOUTHERN CALIFORNIA View publication Active
Mapping proximal and distal splicing-regulatory elements HG012359 ZHANG, CHAOLIN COLUMBIA UNIVERSITY HEALTH SCIENCES View publication Active
Light-Seq: Spatially targeted profiling of transcriptomic states in cells and tissue HG012926 YIN, PENG HARVARD UNIVERSITY View publication Active
In vivo Perturb-map: scalable genetic screens with single-cell and spatial resolution in intact tissues HG012819 JIN, XIN SCRIPPS RESEARCH INSTITUTE, THE View publication Active
Next generation massively multiplexed combinatorial genetic screens HG012351 MALI, PRASHANT (contact); IDEKER, TREY UNIVERSITY OF CALIFORNIA, SAN DIEGO View publication Active
Mechanisms of Transcriptional Control Revealed by Nascent Transcript Sequencing HG007173 CHURCHMAN, LEE STIRLING HARVARD MEDICAL SCHOOL View publication Active
Extensive multiplexing of protein nucleic-acid interactions to comprehensively study gene expression regulation from chromatin to mRNA degradation HG012216 JOVANOVIC, MARKO (contact); GUTTMAN, MITCHELL COLUMBIA UNIV NEW YORK MORNINGSIDE View publication Active
Mapping the dynamics of mouse neurogenesis in autism models using high-resolution genomic barcoding technologies HG012357 KALHOR, REZA JOHNS HOPKINS UNIVERSITY View publication Active
Targets and functions of the mammalian snoRNAome HG012780 PAN, TAO (contact); HE, CHUAN UNIVERSITY OF CHICAGO View publication Active
Ultrasensitive multiomic platform using epitope-targeted DNA methylation mapping HG011875 KEOGH, MICHAEL-CHRISTOPHER (contact); VENTERS, BRYAN J EPICYPHER, INC. View publication Active
Methods for Mapping Genetic Regulatory Elements in Single Cells and Single Molecules HG012383 STREETS, AARON UNIVERSITY OF CALIFORNIA BERKELEY View publication Active
High-throughput analysis of the effects of gene promoters and chromosomal environments on single-cell gene expression HG012304 COHEN, BARAK A WASHINGTON UNIVERSITY View publication Active
High-throughput development and characterization of compact tools for transcriptional and chromatin perturbations HG011866 BINTU, LACRAMIOARA (contact); BASSIK, MICHAEL C STANFORD UNIVERSITY View publication Active
Versatile, exponentially scalable methods for single cell molecular profiling HG010632 SHENDURE, JAY ASHOK (contact); TRAPNELL, BRUCE COLSTON UNIVERSITY OF WASHINGTON View publication Active
A rapid method for global and targeted miRNA next generation sequencing HG013444 RAO, VARSHA CLARET BIOSCIENCE, LLC View publication Complete
Integrated experimental and statistical tools for ultra-high-throughput spatial transcriptomics HG013180 HAN, HEE-SUN UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN View publication Complete
A quick, and robust, and unbiased platform for circular RNAs isolation, discovery and profiling. HG013073 KHADE, PRASHANT K RIBO-THERAPEUTICS LLC View publication Complete
Post-translational phenotypic profiling through nucleotide barcode sequencing HG012991 INGOLIA, NICHOLAS T UNIVERSITY OF CALIFORNIA BERKELEY View publication Complete
Rapid NGS Method for Mapping of the Epitranscriptome HG012534 STENGEL, GUDRUN ALIDA BIOSCIENCES, INC. View publication Complete
Developing a robust method for analyzing transcription factor mediated chromatin interactions HG012627 CHEN, LIN UNIVERSITY OF SOUTHERN CALIFORNIA View publication Complete
Multiplexed Analysis of the Epitranscriptome HG012170 STENGEL, GUDRUN ALIDA BIOSCIENCES, INC. View publication Complete
Scalable, quantitative, single-cell CRISPR screens HG012230 NORMAN, THOMAS SLOAN-KETTERING INST CAN RESEARCH View publication Complete
Bi-functional photo-crosslinking (BFPX) for genome-wide study of protein-nucleic acid interactions HG012419 CHEN, LIN UNIVERSITY OF SOUTHERN CALIFORNIA View publication Complete
Advancing an Innovative NGS Approach to Discover and Investigate Histone Tail Proteolysis HG012833 RICE, JUDD C UNIVERSITY OF SOUTHERN CALIFORNIA View publication Complete
CRISPR-based genome tagging of iPS Cells for stain-free multicolor live cell analysis HG012241 PEREZ-LEAL, OSCAR TEMPLE UNIV OF THE COMMONWEALTH View publication Complete
Single-cell and single-molecule profiling of protein-DNA interactions by MACHA HG012423 POTT, SEBASTIAN (contact); IKEGAMI, KOHTA UNIVERSITY OF CHICAGO View publication Complete
Semi-permeable capsules for high-throughput single cell multi-omics HG012771 KLEIN, ALLON MOSHE HARVARD MEDICAL SCHOOL View publication Complete
A single-strand ligation approach for concomitant DNA and RNA next-generation sequencing from low abundance inputs HG011877 RAO, VARSHA CLARET BIOSCIENCE, LLC View publication Complete
A scalable kit-based assay for multi-omic analyses of transcriptional protein binding and chromatin interactions from ultra-low input frozen and FFPE samples at single-cell resolution HG011897 SCHMITT, ANTHONY ARIMA GENOMICS, INC. View publication Complete
Tagmentation-based Indexing for Methylation Sequencing as a novel method of high-throughput methylation clock measurement HG011850 SINCLAIR, DAVID A HARVARD MEDICAL SCHOOL View publication Complete
Bacteriophage Mu as Tool to Study Genome Organization in Bacteria and Eukaryotes HG011838 HARSHEY, RASIKA M (contact); FREDDOLINO, LYDIA P UNIVERSITY OF TEXAS, AUSTIN View publication Complete
High-throughput detection of transcriptomic and epitranscriptomic variation and kinetics using MarathonRT HG011868 PYLE, ANNA MARIE (contact); GRAVELEY, BRENTON R YALE UNIVERSITY View publication Complete
STAMP technology to enable single-cell and isoform-sensitive detection of RBP sites HG011864 YEO, EUGENE WEI-MING UNIVERSITY OF CALIFORNIA, SAN DIEGO View publication Complete
RNA targeting tools with novel specific RNA-guided RNA-targeting CRISPR effectors HG011857 GOOTENBERG, JONATHAN SAMUEL (contact); ABUDAYYEH, OMAR O MASSACHUSETTS INSTITUTE OF TECHNOLOGY View publication Complete
Nanopore based profiling of epigenetic state HG009190 TIMP, WINSTON GEORGE JOHNS HOPKINS UNIVERSITY View publication Complete
Protein tagging at scale to enable functional genomic studies HG011855 CHAVEZ, ALEJANDRO COLUMBIA UNIVERSITY HEALTH SCIENCES View publication Complete
Development of efficient quantitative chromatin profiling in kit and high-throughput formats HG010640 VENTERS, BRYAN J (contact); KEOGH, MICHAEL-CHRISTOPHER EPICYPHER, INC. View publication Complete
Arrayed single-cell readout of pooled genetic perturbation libraries HG009283 BLAINEY, PAUL CLARK BROAD INSTITUTE, INC. View publication Complete
Next-generation Functional Genetic Screening of Un-screenable Traits HG009285 MALI, PRASHANT (contact); TAMAYO, PABLO ; ZHANG, KUN UNIVERSITY OF CALIFORNIA, SAN DIEGO View publication Complete
Programmable RNA-targeting tools HG009761 ZHANG, FENG BROAD INSTITUTE, INC. View publication Complete
A transposase system for integrative ChIP-exo and ATAC-seq analysis at single-cell resolution HG010211 ZEITLINGER, JULIA STOWERS INSTITUTE FOR MEDICAL RESEARCH View publication Complete
AVATAR: highly parallel analysis of variation in transcription factors and their DNA binding sites HG010200 BULYK, MARTHA L BRIGHAM AND WOMEN’S HOSPITAL View publication Complete
Massively Parallel Single Cell Detection of Rare Variants with Split-Pool Combinatorial Indexing HG011229 KENNEDY, SCOTT ROBERT (contact); SEELIG, GEORG UNIVERSITY OF WASHINGTON View publication Complete
Circular RNA as a platform for genome-wide microRNA sponge libraries HG011214 PICKERING, BRIAN FREDERICK CHIMERNA THERAPEUTICS INC. View publication Complete
Orthocoding for Spatial Sequencing HG011231 SALZMAN, JULIA; FORDYCE, POLLY MORRELL; ROHATGI, RAJAT STANFORD UNIVERSITY View publication Complete
Drop-BS: high-throughput single-cell bisulfite sequencing on a microfluidic droplet platform HG010195 LU, CHANG VIRGINIA POLYTECHNIC INST AND ST UNIV View publication Complete
Development of methods for multi-omic analysis of DNA methylation and chromatin architecture in single cells HG010634 ECKER, JOSEPH R (contact); DIXON, JESSE R SALK INSTITUTE FOR BIOLOGICAL STUDIES View publication Complete
TempO-Seq Profiling of RNA Epitranscriptomic Modifications HG009763 SELIGMANN, BRUCE E. BIOSPYDER TECHNOLOGIES, INC. View publication Complete
Epi-seq: Multiplexed ChIP-seq for personalized medicine and drug discovery HG010237 JELINEK, MARY ANNE ACTIVE MOTIF, INC. View publication Complete
Non-destructive epigenetic sequencing with DNA deaminase enzymes HG010646 KOHLI, RAHUL MANU (contact); WU, HAO UNIVERSITY OF PENNSYLVANIA View publication Complete
A single cell spatial genomics platform for multi-modal characterization of tissue organization HG010647 CHEN, FEI (contact); MACOSKO, EVAN Z BROAD INSTITUTE, INC. View publication Complete
Integrative single-cell spatial genomic, transcriptomic, and epigenetic imaging in mammalian tissue HG011245 WANG, SIYUAN YALE UNIVERSITY View publication Complete
Mapping gene-by-environment interactions using multiplexed single cell RNA-sequencing HG011239 YE, CHUN JIMMIE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO View publication Complete

in conjunction with

The Technology Development Coordinating Center is supported by NHGRI Project U24HG011735 and The Jackson Laboratory.

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