[ { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/e2fjt-agg74", "eprint_status": "archive", "datestamp": "2024-02-05 22:58:51", "lastmod": "2024-02-05 22:58:51", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Du", "given": "Rongrong" }, "orcid": "0009-0003-4942-3020" }, { "name": { "family": "Flynn", "given": "Michael J." } }, { "name": { "family": "Honsa", "given": "Monique" } }, { "name": { "family": "Jungmann", "given": "Ralf" }, "orcid": "0000-0003-4607-3312" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "miRNA circuit modules for tunable dosage compensated gene expression", "ispublished": "unpub", "full_text_status": "public", "abstract": "
This dataset contains the raw data, data processing codes, and figures for the manuscript 'miRNA circuit modules for tunable dosage compensated gene expression'. Bulk RNAseq raw data is available upon request from the authors.
", "date": "2024-02-05", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/e2fjt-agg74", "doi": "10.22002/e2fjt-agg74", "primary_object": { "basename": "Magic_Folder_Manuscript.zip", "url": "https://data.caltech.edu/records/e2fjt-agg74/files/Magic_Folder_Manuscript.zip" }, "resource_type": "dataset", "pub_year": "2024", "author_list": "Du, Rongrong; Flynn, Michael J.; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/pmpby-gpj05", "eprint_status": "archive", "datestamp": "2023-12-13 06:57:29", "lastmod": "2023-12-13 19:05:41", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Chadly", "given": "Duncan M." }, "orcid": "0000-0002-8417-1522" }, { "name": { "family": "Frieda", "given": "Kirsten" } }, { "name": { "family": "Gui", "given": "Chen" }, "orcid": "0000-0002-8975-7610" }, { "name": { "family": "Klock", "given": "Leslie" }, "orcid": "0009-0003-6212-7082" }, { "name": { "family": "Tran", "given": "Martin" }, "orcid": "0000-0001-9882-7230" }, { "name": { "family": "Sui", "given": "Margaret Y." }, "orcid": "0009-0004-4129-0902" }, { "name": { "family": "Takei", "given": "Yodai" }, "orcid": "0000-0002-7226-5185" }, { "name": { "family": "Bouckaert", "given": "Remco" }, "orcid": "0000-0001-6765-3813" }, { "name": { "family": "Lois", "given": "Carlos" }, "orcid": "0000-0002-7305-2317" }, { "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Reconstructing cell histories with image-readable base editor recording: Raw Images", "ispublished": "unpub", "full_text_status": "public", "note": "This dataset contains the raw imaging data from the manuscript, \"Reconstructing cell histories with image-readable base editor recording.\" Analysis scripts and additional data can be found at DOI: 10.22002/327t7-ke088
", "abstract": "Knowing the ancestral states and lineage relationships of individual cells could unravel the dynamic programs underlying development. Engineering cells to actively record information within their own genomic DNA could reveal these histories, but existing recording systems have limited information capacity or disrupt spatial context. Here, we introduce baseMEMOIR, which combines base editing, sequential hybridization imaging, and Bayesian inference to allow reconstruction of high resolution cell lineage trees and cell state dynamics while preserving spatial organization. BaseMEMOIR stochastically and irreversibly edits engineered dinucleotides to one of three alternative image-readable states. By genomically integrating arrays of editable dinucleotides, we constructed an embryonic stem cell line with 792 bits of recordable, image-readable memory. Simulations showed that this memory size was sufficient for accurate reconstruction of deep lineage trees. Experimentally, baseMEMOIR allowed precise reconstruction of lineage trees 6 or more generations deep in embryonic stem cell colonies. Further, it also allowed inference of ancestral cell states and their quantitative cell state transition rates, all from endpoint images. baseMEMOIR thus provides a scalable framework for reconstructing single cell histories in spatially organized multicellular systems.
", "date": "2023-12-12", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/pmpby-gpj05", "doi": "10.22002/pmpby-gpj05", "primary_object": { "basename": "README.txt", "url": "https://data.caltech.edu/records/pmpby-gpj05/files/README.txt" }, "related_objects": [ { "basename": "baseMEMOIR_Images.tar.gz", "url": "https://data.caltech.edu/records/pmpby-gpj05/files/baseMEMOIR_Images.tar.gz" } ], "resource_type": "dataset", "pub_year": "2023", "author_list": "Chadly, Duncan M.; Frieda, Kirsten; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/327t7-ke088", "eprint_status": "archive", "datestamp": "2023-12-13 06:58:29", "lastmod": "2023-12-13 19:04:50", "type": "collection", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Chadly", "given": "Duncan M." }, "orcid": "0000-0002-8417-1522" }, { "name": { "family": "Frieda", "given": "Kirsten" } }, { "name": { "family": "Gui", "given": "Chen" }, "orcid": "0000-0002-8975-7610" }, { "name": { "family": "Klock", "given": "Leslie" }, "orcid": "0009-0003-6212-7082" }, { "name": { "family": "Tran", "given": "Martin" }, "orcid": "0000-0001-9882-7230" }, { "name": { "family": "Sui", "given": "Margaret Y." }, "orcid": "0009-0004-4129-0902" }, { "name": { "family": "Takei", "given": "Yodai" }, "orcid": "0000-0002-7226-5185" }, { "name": { "family": "Bouckaert", "given": "Remco" }, "orcid": "0000-0001-6765-3813" }, { "name": { "family": "Lois", "given": "Carlos" }, "orcid": "0000-0002-7305-2317" }, { "name": { "family": "Cai", "given": "Long" }, "orcid": "0000-0002-7154-5361" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Reconstructing cell histories with image-readable base editor recording: Analysis Code and Supplemental Data", "ispublished": "unpub", "full_text_status": "public", "note": "This dataset contains the data, code, and scripts to reproduce the results in the manuscript, \"Reconstructing cell histories with image-readable base editor recording,\" with the exception of raw microscope images which can be found at doi: 10.22002/pmpby-gpj05
", "abstract": "Knowing the ancestral states and lineage relationships of individual cells could unravel the dynamic programs underlying development. Engineering cells to actively record information within their own genomic DNA could reveal these histories, but existing recording systems have limited information capacity or disrupt spatial context. Here, we introduce baseMEMOIR, which combines base editing, sequential hybridization imaging, and Bayesian inference to allow reconstruction of high resolution cell lineage trees and cell state dynamics while preserving spatial organization. BaseMEMOIR stochastically and irreversibly edits engineered dinucleotides to one of three alternative image-readable states. By genomically integrating arrays of editable dinucleotides, we constructed an embryonic stem cell line with 792 bits of recordable, image-readable memory. Simulations showed that this memory size was sufficient for accurate reconstruction of deep lineage trees. Experimentally, baseMEMOIR allowed precise reconstruction of lineage trees 6 or more generations deep in embryonic stem cell colonies. Further, it also allowed inference of ancestral cell states and their quantitative cell state transition rates, all from endpoint images. baseMEMOIR thus provides a scalable framework for reconstructing single cell histories in spatially organized multicellular systems.
", "date": "2023-12-12", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/327t7-ke088", "doi": "10.22002/327t7-ke088", "primary_object": { "basename": "BaseMEM_Magic.tar.gz", "url": "https://data.caltech.edu/records/327t7-ke088/files/BaseMEM_Magic.tar.gz" }, "related_objects": [ { "basename": "README.txt", "url": "https://data.caltech.edu/records/327t7-ke088/files/README.txt" } ], "resource_type": "collection", "pub_year": "2023", "author_list": "Chadly, Duncan M.; Frieda, Kirsten; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/kas2z-0fe41", "eprint_status": "archive", "datestamp": "2023-10-31 05:37:04", "lastmod": "2023-10-31 05:37:04", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Parres-Gold", "given": "Jacob" }, "orcid": "0000-0002-2050-0139" }, { "name": { "family": "Levine", "given": "Matthew" }, "orcid": "0000-0002-5627-3169" }, { "name": { "family": "Emert", "given": "Benjamin" }, "orcid": "0000-0002-4857-2425" }, { "name": { "family": "Stuart", "given": "Andrew M." }, "orcid": "0000-0001-9091-7266" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Principles of Computation by Competitive Protein Dimerization Networks", "ispublished": "unpub", "full_text_status": "public", "note": "Files available via S3 at https://renc.osn.xsede.org/ini210004tommorrell/kas2z-0fe41/</p>parresgold_2023_dimer_networks_data.tar, 340.2 GB \n<a role=\"button\" class=\"ui compact mini button\" href=\"https://renc.osn.xsede.org/ini210004tommorrell/kas2z-0fe41/parresgold_2023_dimer_networks_data.tar\"\n > <i class=\"download icon\"></i> Download </a>
</p>", "abstract": "Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations, in which the concentrations of monomers (inputs) determine the concentrations of dimers (outputs). Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform (their \"expressivity\") and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks (3-6 monomers) can perform diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough (\u22658 proteins), can perform nearly all (~90%) potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.", "date": "2023-10-20", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/kas2z-0fe41", "doi": "10.22002/kas2z-0fe41", "primary_object": { "basename": "expressivity_paper_README.pdf", "url": "https://data.caltech.edu/records/kas2z-0fe41/files/expressivity_paper_README.pdf" }, "related_objects": [ { "basename": "parresgold_2023_dimer_networks_code.zip", "url": "https://data.caltech.edu/records/kas2z-0fe41/files/parresgold_2023_dimer_networks_code.zip" }, { "basename": "parresgold_2023_dimer_networks_plotting_data.zip", "url": "https://data.caltech.edu/records/kas2z-0fe41/files/parresgold_2023_dimer_networks_plotting_data.zip" } ], "resource_type": "dataset", "pub_year": "2023", "author_list": "Parres-Gold, Jacob; Levine, Matthew; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/kn8yx-kmb24", "eprint_status": "archive", "datestamp": "2023-10-10 17:11:20", "lastmod": "2023-10-10 17:11:20", "type": "collection", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Tran", "given": "Martin" }, "orcid": "0000-0001-9882-7230" }, { "name": { "family": "Askary", "given": "Amjad" } }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Lineage motifs: developmental modules for control of cell type proportions (post-revision)", "ispublished": "unpub", "full_text_status": "public", "note": "This dataset contains the data, code, and scripts to reproduce the results in the manuscript, \"Lineage motifs: developmental modules for control of cell type proportions.\" Within this resource, data and scripts are organized by figure. All code is written in Python, with analysis scripts provided as Jupyter notebooks.
", "abstract": "In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells or extrinsic interactions that produce specific patterns of descendant cell types on lineage trees. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer progenitor states and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell fates on lineage trees as potential signatures of committed progenitor states or extrinsic interactions. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in retina and early embryonic development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.
", "date": "2023-10-10", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/kn8yx-kmb24", "doi": "10.22002/kn8yx-kmb24", "primary_object": { "basename": "linmo_v02.zip", "url": "https://data.caltech.edu/records/kn8yx-kmb24/files/linmo_v02.zip" }, "resource_type": "collection", "pub_year": "2023", "author_list": "Tran, Martin; Askary, Amjad; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/hf6zq-zmg82", "eprint_status": "archive", "datestamp": "2023-08-02 19:22:21", "lastmod": "2023-08-02 19:22:21", "type": "collection", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Granados", "given": "Alejandro A." }, "orcid": "0000-0002-6275-9800" }, { "name": { "family": "Kanrar", "given": "Nivedita" }, "orcid": "0000-0003-0047-951X" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Combinatorial expression motifs in signaling pathways", "ispublished": "unpub", "full_text_status": "public", "keywords": "signaling pathways; combinatorial signaling; promiscuous ligand-receptor interactions; scRNA-seq; motifs", "abstract": "This deposit contains the raw and processed data and documents for the article, 'Combinatorial expression motifs in signaling pathways.' Code and analysis (organized by figure) are available at the GitHub repository https://github.com/nkanrar/motifs and Caltech DATA https://data.caltech.edu/records/bgm15-18g17. Please see the related publication for more details, and contact the corresponding authors with any questions.
", "date": "2023-08-02", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/hf6zq-zmg82", "funders": { "items": [ { "grant_number": "HD075335A" }, { "grant_number": "UWSC10142" }, {} ] }, "doi": "10.22002/hf6zq-zmg82", "primary_object": { "basename": "data.zip", "url": "https://data.caltech.edu/records/hf6zq-zmg82/files/data.zip" }, "related_objects": [ { "basename": "submission.zip", "url": "https://data.caltech.edu/records/hf6zq-zmg82/files/submission.zip" } ], "resource_type": "collection", "pub_year": "2023", "author_list": "Granados, Alejandro A.; Kanrar, Nivedita; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/37gwp-bjg24", "eprint_status": "archive", "datestamp": "2023-08-02 19:00:10", "lastmod": "2023-08-02 19:00:10", "type": "software", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Granados", "given": "Alejandro A." }, "orcid": "0000-0002-6275-9800" }, { "name": { "family": "Kanrar", "given": "Nivedita" }, "orcid": "0000-0003-0047-951X" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "motifs \u2013 0.1.0", "ispublished": "unpub", "full_text_status": "public", "keywords": "combinatorial signaling; GitHub; IGA; motifs; promiscuous ligand-receptor interactions; Python 3; R; scRNA-seq; signaling pathways", "abstract": "This deposit contains the code and analysis for the manuscript, 'Combinatorial expression motifs in signaling pathways.' Data are available at the CaltechDATA repository https://. Please see the related publication for more details, and contact the corresponding authors for any questions.
", "date": "2023-08-01", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/37gwp-bjg24", "doi": "10.22002/37gwp-bjg24", "primary_object": { "basename": "motifs_v0.1.0.zip", "url": "https://data.caltech.edu/records/37gwp-bjg24/files/motifs_v0.1.0.zip" }, "resource_type": "software", "pub_year": "2023", "author_list": "Granados, Alejandro A.; Kanrar, Nivedita; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/htgfr-11t35", "eprint_status": "archive", "datestamp": "2023-05-18 01:53:37", "lastmod": "2023-05-18 01:53:56", "type": "collection", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Tran", "given": "Martin" }, "orcid": "0000-0001-9882-7230" }, { "name": { "family": "Askary", "given": "Amjad" } }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Lineage motifs: developmental modules for control of cell type proportions", "ispublished": "unpub", "full_text_status": "restricted", "note": "This dataset contains the data, code, and scripts to reproduce the results in the manuscript, \"Lineage motifs: developmental modules for control of cell type proportions.\" Within this resource, data and scripts are organized by figure. All code is written in Python, with analysis scripts provided as Jupyter notebooks.
", "abstract": "In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells that produce specific sets of descendant cell types. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer progenitor states and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell types on lineage trees as potential signatures of committed progenitor states. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in retina and early embryonic development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.
", "date": "2023-05-16", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/htgfr-11t35", "doi": "10.22002/htgfr-11t35", "primary_object": { "basename": "linmo.zip", "url": "https://data.caltech.edu/records/htgfr-11t35/files/linmo.zip" }, "resource_type": "collection", "pub_year": "2023", "author_list": "Tran, Martin; Askary, Amjad; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/0sdrn-73r13", "eprint_status": "archive", "datestamp": "2023-04-26 04:33:21", "lastmod": "2023-04-26 04:33:21", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "name": { "family": "Santat", "given": "Leah A." }, "orcid": "0000-0003-0511-9740" }, { "name": { "family": "Markson", "given": "Joseph S." }, "orcid": "0000-0002-3167-3887" }, { "name": { "family": "Nandagopal", "given": "Nagarajan" }, "orcid": "0000-0002-0469-6549" }, { "name": { "family": "Gregrowicz", "given": "Jan" } }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "[Revision] Reconstitution of morphogen shuttling circuits", "ispublished": "unpub", "full_text_status": "public", "abstract": "Here we provide raw data, code, and other supplementary material related to the manuscript, \"Reconstitution of morphogen shuttling circuits,\" by Ronghui Zhu et al. This includes computer codes for implementing the shuttling model, maps of constructs used in this manuscript, raw imaging and flow cytometry data, and raw time-lapse images.
", "date": "2023-04-24", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/0sdrn-73r13", "doi": "10.22002/0sdrn-73r13", "primary_object": { "basename": "Constructs used in the study.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Constructs used in the study.zip" }, "related_objects": [ { "basename": "Revision_Shuttling modeling.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Revision_Shuttling modeling.zip" }, { "basename": "Revision_Shuttling movies.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Revision_Shuttling movies.zip" }, { "basename": "Gradient Movie Rep3.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Gradient Movie Rep3.zip" }, { "basename": "Revision_Readme.txt", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Revision_Readme.txt" }, { "basename": "Revision_Shuttling data except for movies.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Revision_Shuttling data except for movies.zip" }, { "basename": "rBMP4 Movie (MovieS2to4).zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/rBMP4 Movie (MovieS2to4).zip" }, { "basename": "Gradient Movie Background.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Gradient Movie Background.zip" }, { "basename": "Gradient Movie Rep1.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Gradient Movie Rep1.zip" }, { "basename": "Gradient Movie Rep2.zip", "url": "https://data.caltech.edu/records/0sdrn-73r13/files/Gradient Movie Rep2.zip" } ], "resource_type": "dataset", "pub_year": "2023", "author_list": "Zhu, Ronghui; Santat, Leah A.; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/jdw94-3nh81", "eprint_status": "archive", "datestamp": "2023-05-10 02:34:21", "lastmod": "2023-08-10 05:42:29", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Ma", "given": "Yitong" }, "orcid": "0000-0003-4446-7326" }, { "name": { "family": "Budde", "given": "Mark" } }, { "name": { "family": "Zhu", "given": "Junqin" }, "orcid": "0000-0002-8159-6402" }, { "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density", "ispublished": "unpub", "full_text_status": "public", "abstract": "Raw data for paper \"Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density\". Previously titled as \"Promoter CpG content regulates DNMT-dependent silencing dynamics\"
", "date": "2023", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/jdw94-3nh81", "doi": "10.22002/jdw94-3nh81", "primary_object": { "basename": "Plasmids_gb_files.zip", "url": "https://data.caltech.edu/records/jdw94-3nh81/files/Plasmids_gb_files.zip" }, "related_objects": [ { "basename": "Flow Data and Analysis for Figure 2 and S2.zip", "url": "https://data.caltech.edu/records/jdw94-3nh81/files/Flow Data and Analysis for Figure 2 and S2.zip" }, { "basename": "Flow Data and Analysis for Figure 3D S3B.zip", "url": "https://data.caltech.edu/records/jdw94-3nh81/files/Flow Data and Analysis for Figure 3D S3B.zip" }, { "basename": "Sequencing and Analysis for Figure 3.zip", "url": "https://data.caltech.edu/records/jdw94-3nh81/files/Sequencing and Analysis for Figure 3.zip" } ], "resource_type": "dataset", "pub_year": "2023", "author_list": "Ma, Yitong; Budde, Mark; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/4y293-6eg49", "eprint_status": "archive", "datestamp": "2022-11-16 04:37:16", "lastmod": "2022-11-16 04:37:16", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Wang", "given": "Sheng" }, "orcid": "0000-0002-4070-7313" }, { "name": { "family": "Garcia-Ojalvo", "given": "Jordi" }, "orcid": "0000-0002-3716-7520" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Periodic spatial patterning with a single morphogen", "ispublished": "unpub", "full_text_status": "public", "abstract": "Data and code repository for paper \"Periodic spatial patterning with a single morphogen\"
", "date": "2022-11-16", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/4y293-6eg49", "doi": "10.22002/4y293-6eg49", "primary_object": { "basename": "ModelCode.zip", "url": "https://data.caltech.edu/records/4y293-6eg49/files/ModelCode.zip" }, "related_objects": [ { "basename": "SimulationData.zip", "url": "https://data.caltech.edu/records/4y293-6eg49/files/SimulationData.zip" } ], "resource_type": "dataset", "pub_year": "2022", "author_list": "Wang, Sheng; Garcia-Ojalvo, Jordi; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/hwv5v-m9x76", "eprint_status": "archive", "datestamp": "2022-09-10 05:43:32", "lastmod": "2022-11-18 17:38:22", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Wang", "given": "Sheng" }, "orcid": "0000-0002-4070-7313" }, { "name": { "family": "Garc\u00eda-Ojalvo", "given": "Jordi" }, "orcid": "0000-0002-3716-7520" }, { "name": { "family": "Elowitz", "given": "Michael B" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Periodic spatial patterning with a single morphogen", "ispublished": "unpub", "full_text_status": "public", "keywords": "single morphogen; spatial patterning", "abstract": "Data and code repository for paper \"Periodic spatial patterning with a single morphogen\"", "date": "2022-03-16", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/hwv5v-m9x76", "doi": "10.22002/D1.20060", "primary_object": { "basename": "ModelCode.zip", "url": "https://data.caltech.edu/records/hwv5v-m9x76/files/ModelCode.zip" }, "related_objects": [ { "basename": "SimulationData.zip", "url": "https://data.caltech.edu/records/hwv5v-m9x76/files/SimulationData.zip" } ], "resource_type": "dataset", "pub_year": "2022", "author_list": "Wang, Sheng; Garc\u00eda-Ojalvo, Jordi; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/s7epj-5ry14", "eprint_status": "archive", "datestamp": "2022-09-12 22:05:30", "lastmod": "2022-11-18 17:37:22", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Zhu", "given": "Ronghui" }, "orcid": "0000-0001-8171-482X" }, { "name": { "family": "del Rio-Salgado", "given": "Jesus M." } }, { "name": { "family": "Garc\u00eda-Ojalvo", "given": "Jordi" }, "orcid": "0000-0002-3716-7520" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic multistability in mammalian cells", "ispublished": "unpub", "full_text_status": "public", "keywords": "Synthetic Multistability", "abstract": "Data and code repository for paper \"Synthetic multistability in mammalian cells\"", "date": "2021-02-09", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/s7epj-5ry14", "doi": "10.22002/D1.1882", "primary_object": { "basename": "DataFigs.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/DataFigs.zip" }, "related_objects": [ { "basename": "ModelFigs.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/ModelFigs.zip" }, { "basename": "ModelingAndDataProcessingCodes.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/ModelingAndDataProcessingCodes.zip" }, { "basename": "MultiFate2movierawdata.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/MultiFate2movierawdata.zip" }, { "basename": "MultiFate3movierawdata.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/MultiFate3movierawdata.zip" }, { "basename": "ConstructMaps.zip", "url": "https://data.caltech.edu/records/s7epj-5ry14/files/ConstructMaps.zip" } ], "resource_type": "dataset", "pub_year": "2021", "author_list": "Zhu, Ronghui; del Rio-Salgado, Jesus M.; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/4ry4k-5gf89", "eprint_status": "archive", "datestamp": "2022-09-08 22:34:02", "lastmod": "2022-11-18 19:47:41", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Klumpe", "given": "Heidi" }, "orcid": "0000-0001-8938-2006" }, { "name": { "family": "Langley", "given": "Matthew A." }, "orcid": "0000-0003-2890-5584" }, { "name": { "family": "Linton", "given": "James M." } }, { "name": { "family": "Su", "given": "Christina J." }, "orcid": "0000-0002-9223-9777" }, { "name": { "family": "Antebi", "given": "Yaron E." }, "orcid": "0000-0002-5771-6814" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "orcid": "0000-0002-1221-0967" } ] }, "title": "The context-dependent, combinatorial logic of BMP signaling", "ispublished": "unpub", "full_text_status": "public", "keywords": "bone morphogenetic protein; BMP; signaling pathways; cell context; combinatorial signaling; promiscuous receptor-ligand interactions; pairwise interaction analysis", "note": "This deposit contains the data, code, and analysis to recreate the results in the manuscript, 'The combinatorial logic of BMP signaling across contexts.' The processed data and analysis are organized by figures, and the raw data are organized by data type. The code and analysis are written for Matlab 2019a and Python 3. Please see the related publication for more details, and contact the corresponding authors for any questions.\n\nKlumpe, H., Langley, M.A., Linton, J.M., Su, C.J. Antebi, Y.E., Elowitz, M.B. (2020). The combinatorial logic of BMP signaling across contexts (Version 1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.1693\nor choose a different citation style.", "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.", "date": "2020-12-05", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/4ry4k-5gf89", "doi": "10.22002/D1.1693", "primary_object": { "basename": "equivalence_paper_analysis.zip", "url": "https://data.caltech.edu/records/4ry4k-5gf89/files/equivalence_paper_analysis.zip" }, "related_objects": [ { "basename": "equivalence_paper_code_and_data_README.pdf", "url": "https://data.caltech.edu/records/4ry4k-5gf89/files/equivalence_paper_code_and_data_README.pdf" }, { "basename": "equivalence_paper_data.zip", "url": "https://data.caltech.edu/records/4ry4k-5gf89/files/equivalence_paper_data.zip" }, { "basename": "matlab_functions.zip", "url": "https://data.caltech.edu/records/4ry4k-5gf89/files/matlab_functions.zip" } ], "resource_type": "dataset", "pub_year": "2020", "author_list": "Klumpe, Heidi; Langley, Matthew A.; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/5e4cj-34824", "eprint_status": "archive", "datestamp": "2022-09-08 22:31:23", "lastmod": "2022-11-29 00:12:53", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Su", "given": "Christina" }, "orcid": "0000-0002-9223-9777" }, { "name": { "family": "Murugan", "given": "Arvind" }, "orcid": "0000-0001-5464-917X" }, { "name": { "family": "Linton", "given": "James" } }, { "name": { "family": "Yeluri", "given": "Akshay" }, "orcid": "0000-0001-8654-1673" }, { "name": { "family": "Bois", "given": "Justin" }, "orcid": "0000-0001-7137-8746" }, { "name": { "family": "Klumpe", "given": "Heidi" }, "orcid": "0000-0001-8938-2006" }, { "name": { "family": "Langley", "given": "Matthew" } }, { "name": { "family": "Antebi", "given": "Yaron" }, "orcid": "0000-0002-5771-6814" }, { "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Ligand-receptor promiscuity enables cellular addressing", "ispublished": "unpub", "full_text_status": "public", "keywords": "Bone morphogenetic protein; BMP; Signaling pathways; Communication systems; Information theory; Promiscuity", "note": "This dataset contains the data, code, and scripts to reproduce the results in the manuscript, \"Ligand-receptor promiscuity enables cellular addressing.\" Within this resource, data and scripts are organized by figure. All code is written in Python, with analysis scripts provided as Jupyter notebooks.", "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.", "date": "2020-12-04", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/5e4cj-34824", "doi": "10.22002/D1.1692", "primary_object": { "basename": "CombinatorialAddressing.zip", "url": "https://data.caltech.edu/records/5e4cj-34824/files/CombinatorialAddressing.zip" }, "resource_type": "dataset", "pub_year": "2020", "author_list": "Su, Christina; Murugan, Arvind; et el." }, { "id": "https:/data.caltech.eduhttps://data.caltech.edu/records/jheg8-nad74", "eprint_status": "archive", "datestamp": "2022-09-12 15:55:10", "lastmod": "2023-02-23 03:28:16", "type": "dataset", "metadata_visibility": "show", "creators": { "items": [ { "name": { "family": "Ma", "given": "Yitong" }, "orcid": "0000-0003-4446-7326" }, { "name": { "family": "Budde", "given": "Mark" }, "orcid": "0000-0002-4359-1424" }, { "name": { "family": "Mayalu", "given": "Micha\u00eblle" }, "orcid": "0000-0002-9678-0157" }, { "name": { "family": "Zhu", "given": "Junqin" } }, { "name": { "family": "Murray", "given": "Richard" }, "orcid": "0000-0002-5785-7481" }, { "name": { "family": "Elowitz", "given": "Michael" }, "orcid": "0000-0002-1221-0967" } ] }, "title": "Synthetic mammalian signaling circuits for robust cell population control", "ispublished": "unpub", "full_text_status": "public", "keywords": "Synthetic biology; Quorum sensing", "abstract": "Synthetic signaling circuits could allow engineered cells to sense and control their own population density. The ideal circuit would operate independently of endogenous pathways and be robust to selection pressure for mutations that allow cells to evade population size limits. Here, we show that the plant hormone auxin can be repurposed as an orthogonal communication channel and linked to pathways that control cell survival and death to create synthetic mammalian population control circuits. We identified enzymes, transporters, and other components that allow sending and receiving of two auxin variants. Using these components, we constructed a synthetic quorum sensing system and coupled it to regulation of antibiotic resistance to limit cell population size. Because this population control circuit was susceptible to mutations in signal sensing, we then designed a paradoxical population control circuit, in which auxin both stimulates and inhibits net cell growth at different concentrations. This design provides evolutionarily robust control in a 43 day continuous culture experiment. These results demonstrate robust synthetic population control in mammalian cells and establish a foundation for future cell therapies that can respond to and control their own population sizes within multicellular organisms.", "date": "2020-08-29", "date_type": "published", "publisher": "CaltechDATA", "official_url": "https://data.caltech.edu/records/jheg8-nad74", "funders": { "items": [ { "agency": "Federal", "grant_number": "HR0011-17-0008" } ] }, "doi": "10.22002/D1.1613", "primary_object": { "basename": "Figure 1C 1D 2E 3A-D S1C S1D S2A S2B S2D S3D (Flowcytomety data).zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Figure 1C 1D 2E 3A-D S1C S1D S2A S2B S2D S3D (Flowcytomety data).zip" }, "related_objects": [ { "basename": "Movie S1 Data and Analysis.zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S1 Data and Analysis.zip" }, { "basename": "Movie S3.avi", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S3.avi" }, { "basename": "Movie S4.avi", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S4.avi" }, { "basename": "Movie S4 Data and Analysis.zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S4 Data and Analysis.zip" }, { "basename": "RNAseq Data and Analysis.zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/RNAseq Data and Analysis.zip" }, { "basename": "Figure 1C 1D 2E 3A-D S1C S1D S2A S2B S2D S3D (Analysis).zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Figure 1C 1D 2E 3A-D S1C S1D S2A S2B S2D S3D (Analysis).zip" }, { "basename": "Movie S1.avi", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S1.avi" }, { "basename": "Movie S2.mp4", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S2.mp4" }, { "basename": "Movie S3 Data and Analysis.zip", "url": "https://data.caltech.edu/records/jheg8-nad74/files/Movie S3 Data and Analysis.zip" } ], "resource_type": "dataset", "pub_year": "2020", "author_list": "Ma, Yitong; Budde, Mark; et el." } ]