This dataset contains the updated data, code, and scripts to reproduce the results in the manuscript, \"Genome-wide chromatin recording resolves dynamic cell state changes.\"
", "doi": "10.22002/abcrz-g3683", "publisher": "CaltechDATA", "publication_date": "2026-04-29" }, { "id": "data:8zr8w-t0f77", "collection": "data", "collection_id": "8zr8w-t0f77", "cite_using_url": "https://data.caltech.edu/records/8zr8w-t0f77", "type": "collection", "title": "Engineering RNA export for measurement and manipulation of living cells", "author": [ { "family_name": "Horns", "given_name": "Felix" }, { "family_name": "Martinez", "given_name": "Joe A." }, { "family_name": "Fan", "given_name": "Chengcheng" }, { "family_name": "Haque", "given_name": "Mehernaz" }, { "family_name": "Linton", "given_name": "James M.", "orcid": "0009-0008-2626-1803" }, { "family_name": "Tobin", "given_name": "Victoria" }, { "family_name": "Santat", "given_name": "Leah" }, { "family_name": "Maggiolo", "given_name": "Ailiena O." }, { "family_name": "Bjorkman", "given_name": "Pamela J." }, { "family_name": "Lois", "given_name": "Carlos" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967" } ], "abstract": "Overview This repository contains code and data for analysis and plotting related to the development of synthetic RNA export systems and their application for non-destructive measurement of cell dynamics and delivering RNA from cell to cell. Citation If you use this code, please cite this paper. Horns et al., Engineering RNA export for measurement and manipulation of living cells, Cell 186 (2023). Organization The repository is organized into directories that contain code and data, as described below. analysis: Analysis code to generate figures. imaging_data: Images used for analysis. pipelines: Pipelines for preprocessing sequencing reads. preprocessed_data: Preprocessed data (qPCR, flow cytometry, sequencing, etc.). raw_sequencing_data: Sequencing reads. resources: Software and reference data. sequencing_data_preprocessing: Working directory for pipelines for preprocessing sequencing reads. Environment The primary environment uses Python 3.7.7 and is specified in analysis/environment.yml. Use of the Conda package manger is recommended. Disclaimer This project is not maintained. Software is provided as is and requests for support may not be addressed. Contact If you have questions or comments, please contact Felix Horns at rfhorns@gmail.com.
", "doi": "10.22002/8zr8w-t0f77", "publisher": "CaltechDATA", "publication_date": "2023-07-11" }, { "id": "data:npsbx-rgm79", "collection": "data", "collection_id": "npsbx-rgm79", "cite_using_url": "https://data.caltech.edu/records/npsbx-rgm79", "type": "software", "title": "Kin Correlation Analysis Code and Data", "author": [ { "family_name": "Hormoz", "given_name": "Sahand" }, { "family_name": "Singer", "given_name": "Zakary" }, { "family_name": "Linton", "given_name": "James", "orcid": "0009-0008-2626-1803" }, { "family_name": "Antebi", "given_name": "Yaron" }, { "family_name": "Shraiman", "given_name": "Boris" }, { "family_name": "Elowitz", "given_name": "Michael", "orcid": "0000-0002-1221-0967" } ], "abstract": "This resource provides code and example data for performing Kin Correlation Analysis (KCA), which allows inference of cell state transition rates from lineage information and end-point cell state measurements. See related publication for full information.\n\nMovie_Tracking.zip contains code for cell tracking and lineage visualization. Data_Analysis.zip contains all code for KCA, including scripts and processed data to reproduce analysis figures from the associated publication. In each .zip file, there is a Readme.txt file that provides instructions on using the code.", "doi": "10.22002/D1.1894", "publisher": "CaltechDATA", "publication_date": "2021-02-26" }, { "id": "data:4ry4k-5gf89", "collection": "data", "collection_id": "4ry4k-5gf89", "cite_using_url": "https://data.caltech.edu/records/4ry4k-5gf89", "type": "dataset", "title": "The context-dependent, combinatorial logic of BMP signaling", "author": [ { "family_name": "Klumpe", "given_name": "Heidi", "orcid": "0000-0001-8938-2006" }, { "family_name": "Langley", "given_name": "Matthew A.", "orcid": "0000-0003-2890-5584" }, { "family_name": "Linton", "given_name": "James M.", "orcid": "0009-0008-2626-1803" }, { "family_name": "Su", "given_name": "Christina J.", "orcid": "0000-0002-9223-9777" }, { "family_name": "Antebi", "given_name": "Yaron E.", "orcid": "0000-0002-5771-6814" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967" } ], "abstract": "Cell-cell communication systems typically comprise families of ligand and receptor variants that function together in combinations. Pathway activation depends in a complex way on which ligands are present and what receptors are expressed by the signal-receiving cell. To understand the combinatorial logic of such a system, we systematically measured pairwise Bone Morphogenetic Protein (BMP) ligand interactions in cells with varying receptor expression. Ligands could be classified into equivalence groups based on their profile of positive and negative synergies with other ligands. These groups varied with receptor expression, explaining how ligands can functionally replace each other in one context but not another. Context-dependent combinatorial interactions could be explained by a biochemical model based on competitive formation of alternative signaling complexes with distinct activities. Together, these results provide insights into the roles of BMP combinations in developmental and therapeutic contexts and establish a framework for analyzing other combinatorial, context-dependent signaling systems.
", "doi": "10.22002/D1.1693", "publisher": "CaltechDATA", "publication_date": "2020-12-05" }, { "id": "data:5e4cj-34824", "collection": "data", "collection_id": "5e4cj-34824", "cite_using_url": "https://data.caltech.edu/records/5e4cj-34824", "type": "dataset", "title": "Ligand-receptor promiscuity enables cellular addressing", "author": [ { "family_name": "Su", "given_name": "Christina", "orcid": "0000-0002-9223-9777" }, { "family_name": "Murugan", "given_name": "Arvind", "orcid": "0000-0001-5464-917X" }, { "family_name": "Linton", "given_name": "James", "orcid": "0009-0008-2626-1803" }, { "family_name": "Yeluri", "given_name": "Akshay", "orcid": "0000-0001-8654-1673" }, { "family_name": "Bois", "given_name": "Justin", "orcid": "0000-0001-7137-8746" }, { "family_name": "Klumpe", "given_name": "Heidi", "orcid": "0000-0001-8938-2006" }, { "family_name": "Langley", "given_name": "Matthew" }, { "family_name": "Antebi", "given_name": "Yaron", "orcid": "0000-0002-5771-6814" }, { "family_name": "Elowitz", "given_name": "Michael", "orcid": "0000-0002-1221-0967" } ], "abstract": "In multicellular organisms, secreted ligands selectively activate, or \"address,\" specific target cell populations to control cell fate decision-making and other processes. Key cell-cell communication pathways use multiple promiscuously interacting ligands and receptors, provoking the question of how addressing specificity can emerge from molecular promiscuity. To investigate this issue, we developed a general mathematical modeling framework based on the bone morphogenetic protein (BMP) pathway architecture. We find that promiscuously interacting ligand-receptor systems allow a small number of ligands, acting in combinations, to address a larger number of individual cell types, defined by their receptor expression profiles. Promiscuous systems outperform seemingly more specific one-to-one signaling architectures in addressing capability. Combinatorial addressing extends to groups of cell types, is robust to receptor expression noise, grows more powerful with increasing numbers of receptor variants, and is maximized by specific biochemical parameter relationships. Together, these results identify design principles governing cellular addressing by ligand combinations.
", "doi": "10.22002/D1.1692", "publisher": "CaltechDATA", "publication_date": "2020-12-04" }, { "id": "data:x88dh-6z248", "collection": "data", "collection_id": "x88dh-6z248", "cite_using_url": "https://data.caltech.edu/records/x88dh-6z248", "type": "dataset", "title": "Data for \"In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription \"", "author": [ { "family_name": "Askary", "given_name": "Amjad" }, { "family_name": "Sanchez-Guardado", "given_name": "Luis" }, { "family_name": "Linton", "given_name": "James M.", "orcid": "0009-0008-2626-1803" }, { "family_name": "Chadly", "given_name": "Duncan M." }, { "family_name": "Budde", "given_name": "Mark W." }, { "family_name": "Cai", "given_name": "Long" }, { "family_name": "Lois", "given_name": "Carlos" }, { "family_name": "Elowitz", "given_name": "Michael B.", "orcid": "0000-0002-1221-0967" } ], "abstract": "This dataset provides the raw and analyzed data as well as the code to recreate results reported in the paper \"In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription\". The dataset is organized based on the figures and figure panels of the paper, with the codes provided as Matlab and R scripts. Please contact the corresponding author for any questions or comments regarding the data, the code, the methods, or the reagents used here.", "doi": "10.22002/D1.1303", "publisher": "CaltechDATA", "publication_date": "2019-10-23" } ]