Genomic Technology Development Archives

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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