Genomic Technology Development

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Project Title Project Number Contact PI / Project Leader Organization Name Publications TDCC Status
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
Multiplexed Analysis of the Epitranscriptome HG012170 STENGEL, GUDRUN ALIDA BIOSCIENCES, INC. View publication Active
Mechanisms of Transcriptional Control Revealed by Nascent Transcript Sequencing HG007173 CHURCHMAN, LEE STIRLING HARVARD MEDICAL SCHOOL View publication Active
Scalable, quantitative, single-cell CRISPR screens HG012230 NORMAN, THOMAS SLOAN-KETTERING INST CAN RESEARCH View publication Active
Bi-functional photo-crosslinking (BFPX) for genome-wide study of protein-nucleic acid interactions HG012419 CHEN, LIN UNIVERSITY OF SOUTHERN CALIFORNIA View publication Active
Advancing an Innovative NGS Approach to Discover and Investigate Histone Tail Proteolysis HG012833 RICE, JUDD C UNIVERSITY OF SOUTHERN CALIFORNIA 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
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 Active
Single-cell and single-molecule profiling of protein-DNA interactions by MACHA HG012423 POTT, SEBASTIAN (contact); IKEGAMI, KOHTA 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
Semi-permeable capsules for high-throughput single cell multi-omics HG012771 KLEIN, ALLON MOSHE HARVARD MEDICAL SCHOOL 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
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 Active
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 Active
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 Active
Bacteriophage Mu as Tool to Study Genome Organization in Bacteria and Eukaryotes HG011838 HARSHEY, RASIKA M (contact); FREDDOLINO, PETER L UNIVERSITY OF TEXAS, AUSTIN View publication Active
High-throughput detection of transcriptomic and epitranscriptomic variation and kinetics using MarathonRT HG011868 PYLE, ANNA MARIE (contact); GRAVELEY, BRENTON R YALE UNIVERSITY View publication Active
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 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
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 Active
Nanopore based profiling of epigenetic state HG009190 TIMP, WINSTON GEORGE JOHNS HOPKINS UNIVERSITY View publication Active
Protein tagging at scale to enable functional genomic studies HG011855 CHAVEZ, ALEJANDRO COLUMBIA UNIVERSITY HEALTH SCIENCES View publication Active
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 Active
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 Active
Versatile, exponentially scalable methods for single cell molecular profiling HG010632 SHENDURE, JAY ASHOK (contact); TRAPNELL, BRUCE COLSTON UNIVERSITY OF WASHINGTON View publication Active
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 Active
TempO-Seq Profiling of RNA Epitranscriptomic Modifications HG009763 SELIGMANN, BRUCE E. BIOSPYDER TECHNOLOGIES, INC. View publication Active
Non-destructive epigenetic sequencing with DNA deaminase enzymes HG010646 KOHLI, RAHUL MANU (contact); WU, HAO UNIVERSITY OF PENNSYLVANIA View publication Active
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 Active
Integrative single-cell spatial genomic, transcriptomic, and epigenetic imaging in mammalian tissue HG011245 WANG, SIYUAN YALE UNIVERSITY View publication Active
Mapping gene-by-environment interactions using multiplexed single cell RNA-sequencing HG011239 YE, CHUN JIMMIE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO View publication Active
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
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
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
Epi-seq: Multiplexed ChIP-seq for personalized medicine and drug discovery HG010237 JELINEK, MARY ANNE ACTIVE MOTIF, INC. View publication Complete
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