{
 "naming": "On names: NCBI Taxonomy and LPSN now give the correct species name as Caulobacter vibrioides, with Caulobacter crescentus, the name used in nearly all of the research literature, listed as a synonym. The laboratory strain CB15 (ATCC 19089) and its synchronizable derivative NA1000 are not the type strain of either name.",
 "items": [
  {
   "id": "refseq-nc_011916",
   "name": "NA1000 complete genome (RefSeq chromosome)",
   "category": "genome",
   "strain": "NA1000",
   "description": "Single circular chromosome, 4,042,929 bp. RefSeq NC_011916.1 = GenBank CP001340.1. Curated RefSeq annotation with CCNA_ locus tags (e.g. ctrA = CCNA_03130).",
   "accession": "NC_011916.1",
   "repository": "NCBI RefSeq",
   "url": "https://www.ncbi.nlm.nih.gov/nuccore/NC_011916.1",
   "paperDoi": "10.1128/JB.00255-10",
   "paperCite": "Marks ME et al. 2010 J Bacteriol",
   "status": "live",
   "verified": "E-utilities esummary nuccore NC_011916 -> NC_011916.1 'Caulobacter crescentus NA1000, complete genome', 4042929 bp, taxid 565050, BioSample SAMN02604151; CP001340.1 same title/length."
  },
  {
   "id": "genbank-cp001340",
   "name": "NA1000 complete genome (GenBank/INSDC)",
   "category": "genome",
   "strain": "NA1000",
   "description": "Original INSDC submission of the NA1000 chromosome from Marks et al. 2010 (University of Chicago annotation, CCNA_ locus tags).",
   "accession": "CP001340.1",
   "repository": "GenBank",
   "url": "https://www.ncbi.nlm.nih.gov/nuccore/CP001340.1",
   "paperDoi": "10.1128/JB.00255-10",
   "paperCite": "Marks ME et al. 2010 J Bacteriol",
   "status": "live",
   "verified": "esummary nuccore CP001340 -> 'Caulobacter crescentus NA1000, complete genome', 4042929 bp, taxid 565050."
  },
  {
   "id": "assembly-gcf_000022005",
   "name": "NA1000 genome assembly ASM2200v1",
   "category": "genome",
   "strain": "NA1000",
   "description": "RefSeq reference genome for the species. GCF_000022005.1 paired with GCA_000022005.1; 1 chromosome, 4.04 Mb; RefSeq annotation 3,886 protein-coding genes (released 2020-12-10).",
   "accession": "GCF_000022005.1",
   "repository": "NCBI Datasets",
   "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000022005.1/",
   "paperDoi": "10.1128/JB.00255-10",
   "paperCite": "Marks ME et al. 2010 J Bacteriol",
   "status": "live",
   "verified": "NCBI Datasets v2 dataset_report: GCF_000022005.1 / GCA_000022005.1, ASM2200v1, 'Caulobacter vibrioides NA1000', refseq_category 'reference genome', Complete Genome, annotation provider NCBI RefSeq 2020-12-10. BioProjects PRJNA32027 (sequencing), PRJNA59307 (RefSeq)."
  },
  {
   "id": "refseq-nc_002696",
   "name": "CB15 complete genome (RefSeq chromosome)",
   "category": "genome",
   "strain": "CB15",
   "description": "Single circular chromosome, 4,016,947 bp. RefSeq NC_002696.2 = GenBank AE005673.1. RefSeq re-annotated by PGAP (2025-04-26) with CC_RS locus tags; original CC_ tags kept as old locus tags.",
   "accession": "NC_002696.2",
   "repository": "NCBI RefSeq",
   "url": "https://www.ncbi.nlm.nih.gov/nuccore/NC_002696.2",
   "paperDoi": "10.1073/pnas.061029298",
   "paperCite": "Nierman WC et al. 2001 PNAS",
   "status": "live",
   "verified": "esummary nuccore NC_002696 -> NC_002696.2 'Caulobacter vibrioides CB15, complete sequence', 4016947 bp, taxid 190650. Datasets annotation_report: ctrA locus_tag CC_RS15840 (Gene record lists old tag CC_3035)."
  },
  {
   "id": "genbank-ae005673",
   "name": "CB15 complete genome (GenBank/INSDC, TIGR)",
   "category": "genome",
   "strain": "CB15",
   "description": "Original TIGR genome submission from Nierman et al. 2001, with the classic CC_#### locus tags used in most pre-2010 literature.",
   "accession": "AE005673.1",
   "repository": "GenBank",
   "url": "https://www.ncbi.nlm.nih.gov/nuccore/AE005673.1",
   "paperDoi": "10.1073/pnas.061029298",
   "paperCite": "Nierman WC et al. 2001 PNAS",
   "status": "live",
   "verified": "esummary nuccore AE005673 -> AE005673.1 'Caulobacter crescentus CB15, complete genome', 4016947 bp, taxid 190650."
  },
  {
   "id": "assembly-gcf_000006905",
   "name": "CB15 genome assembly ASM690v1",
   "category": "genome",
   "strain": "CB15",
   "description": "GCF_000006905.1 paired with GCA_000006905.1; 1 chromosome, 4.02 Mb. Current RefSeq annotation GCF_000006905.1-RS_2025_04_26 (PGAP 6.10): 3,823 protein-coding genes, 120 pseudogenes.",
   "accession": "GCF_000006905.1",
   "repository": "NCBI Datasets",
   "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006905.1/",
   "paperDoi": "10.1073/pnas.061029298",
   "paperCite": "Nierman WC et al. 2001 PNAS",
   "status": "live",
   "verified": "NCBI Datasets v2 dataset_report: GCF_000006905.1 / GCA_000006905.1, ASM690v1, 'Caulobacter vibrioides CB15', Complete Genome, released 2002-03-06; annotation RS_2025_04_26. BioProjects PRJNA298, PRJNA57891."
  },
  {
   "id": "assembly-gcf_002858865",
   "name": "Type strain DSM 9893 (CB51) draft genome",
   "category": "genome",
   "strain": "DSM 9893 (CB51)",
   "description": "Draft (25 contigs, 3.97 Mb) genome of the Caulobacter vibrioides type strain; NCBI flags it 'assembly from type material'. Not the CB15 lineage.",
   "accession": "GCF_002858865.1",
   "repository": "NCBI Datasets",
   "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002858865.1/",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "Datasets dataset_report: GCF_002858865.1 ASM285886v1, strain DSM 9893, Contig level, 25 contigs, submitter Beijing Academy of Agriculture and Forestry Science, type_material TYPE_MATERIAL."
  },
  {
   "id": "assembly-gcf_002310295",
   "name": "Strain CB2 complete genome (former C. crescentus type strain)",
   "category": "genome",
   "strain": "CB2",
   "description": "Complete 4.12 Mb genome of CB2 (ATCC 15252 / DSM 4727), type strain of the synonym C. crescentus; NCBI flags it 'assembly from heterotypic synonym type material'.",
   "accession": "GCF_002310295.2",
   "repository": "NCBI Datasets",
   "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002310295.2/",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "Datasets dataset_report: GCF_002310295.2 ASM231029v2, strain CB2, Complete Genome, University of South Carolina, 2018-02-20, PRJNA386178, type_material TYPE_MATERIAL_SYN."
  },
  {
   "id": "ncbi-taxonomy-155892",
   "name": "NCBI Taxonomy: Caulobacter vibrioides (species)",
   "category": "database",
   "strain": "species",
   "description": "Species node 155892 'Caulobacter vibrioides', synonym 'Caulobacter crescentus'. Strain nodes: CB15 = 190650, NA1000 = 565050.",
   "accession": "155892",
   "repository": "NCBI Taxonomy",
   "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=155892",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "esummary/efetch taxonomy 155892,190650,565050 -> 'Caulobacter vibrioides' (species), 'Caulobacter vibrioides CB15' (strain; synonyms C. crescentus CB15, C. vibrioides ATCC 19089), 'Caulobacter vibrioides NA1000' (strain)."
  },
  {
   "id": "ncbi-taxonomy-190650",
   "name": "NCBI Taxonomy: strain CB15",
   "category": "database",
   "strain": "CB15",
   "description": "Strain-level taxid for CB15 (ATCC 19089). Used by STRING, UniProt UP000001816, KEGG ccr.",
   "accession": "190650",
   "repository": "NCBI Taxonomy",
   "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=190650",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "efetch taxonomy 190650 -> ScientificName 'Caulobacter vibrioides CB15', Rank strain."
  },
  {
   "id": "ncbi-taxonomy-565050",
   "name": "NCBI Taxonomy: strain NA1000",
   "category": "database",
   "strain": "NA1000",
   "description": "Strain-level taxid for NA1000 (CB15N). Used by UniProt UP000001364, KEGG ccs and most post-2010 GEO submissions.",
   "accession": "565050",
   "repository": "NCBI Taxonomy",
   "url": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=565050",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "efetch taxonomy 565050 -> ScientificName 'Caulobacter vibrioides NA1000', Rank strain."
  },
  {
   "id": "ncbi-gene-na1000",
   "name": "NCBI Gene: NA1000 genes",
   "category": "database",
   "strain": "NA1000",
   "description": "Gene records for the NA1000 RefSeq annotation (CCNA_ locus tags). Note: legacy CB15 Gene IDs (e.g. ctrA 941285) are discontinued after the CB15 PGAP re-annotation.",
   "accession": null,
   "repository": "NCBI Gene",
   "url": "https://www.ncbi.nlm.nih.gov/gene/?term=txid565050%5BOrganism%3Anoexp%5D",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "esearch gene ctrA AND txid565050 -> GeneID 7330968 (ctrA, alias CCNA_03130, NC_011916.1). Datasets gene API on CB15 GeneID 941285 -> 'DISCONTINUED_GENE_ID'."
  },
  {
   "id": "paper-laub2000",
   "name": "Cell-cycle transcriptome, DNA microarrays (Laub 2000)",
   "category": "transcriptome",
   "strain": "synchronized cells (strain: see paper)",
   "description": "Genome-wide cell-cycle expression in synchronized cells: 553 genes (19% of the genome) vary with the cell cycle. Predates GEO; no GEO/ArrayExpress record found: data in supplementary material.",
   "accession": null,
   "repository": "Supplementary (Science)",
   "url": "https://doi.org/10.1126/science.290.5499.2144",
   "paperDoi": "10.1126/science.290.5499.2144",
   "paperCite": "Laub MT et al. 2000 Science",
   "status": "live",
   "verified": "PubMed 11118148 'Global analysis of the genetic network controlling a bacterial cell cycle'; elink pubmed->gds/sra/bioproject returned no links; DOI resolves (doi.org handle API)."
  },
  {
   "id": "geo-gpl10149",
   "name": "CauloHi1 Affymetrix tiling array platform (McGrath 2007)",
   "category": "transcriptome",
   "strain": "NA1000",
   "description": "Custom Affymetrix 16.6K Caulobacter tiling array described in McGrath 2007 (TSS mapping, cell-cycle transcription). The paper's own data are supplementary; GEO holds the platform used by later series.",
   "accession": "GPL10149",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL10149",
   "paperDoi": "10.1038/nbt1294",
   "paperCite": "McGrath PT et al. 2007 Nat Biotechnol",
   "status": "live",
   "verified": "GEO GPL10149 text: 'Stanford Affymetrix Caulobacter crescentus 16.6K CauloHi1', organism Caulobacter vibrioides, Platform_pubmed_id 17401361; elink pubmed 17401361 -> only GPL10149/GPL11304, no GSE."
  },
  {
   "id": "geo-gse1135",
   "name": "GcrA depletion microarrays (Holtzendorff 2004)",
   "category": "transcriptome",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "Microarray expression profiling after depletion of the cell-cycle regulator GcrA; supporting data for 'Oscillating global regulators control the genetic circuit driving a bacterial cell cycle'.",
   "accession": "GSE1135",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1135",
   "paperDoi": "10.1126/science.1095191",
   "paperCite": "Holtzendorff J et al. 2004 Science",
   "status": "live",
   "verified": "GEO GSE1135: 'GcrA depletion study (Caulobacter vibrioides)', Expression profiling by array, taxid 155892, pubmed 15087506, 13 samples."
  },
  {
   "id": "geo-gse3171",
   "name": "DnaA cell-cycle transcription microarrays (Hottes 2005)",
   "category": "transcriptome",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "Microarray data showing DnaA coordinates replication initiation with cell-cycle transcription.",
   "accession": "GSE3171",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3171",
   "paperDoi": "10.1111/j.1365-2958.2005.04912.x",
   "paperCite": "Hottes AK et al. 2005 Mol Microbiol",
   "status": "live",
   "verified": "GEO GSE3171: 'DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus', taxid 155892, pubmed 16313620, 83 samples."
  },
  {
   "id": "geo-gse22062",
   "name": "SciP microarrays (Gora 2010)",
   "category": "transcriptome",
   "strain": "CB15 (GEO tag)",
   "description": "Expression arrays for SciP, a G1-phase inhibitor of CtrA-dependent transcription.",
   "accession": "GSE22062",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22062",
   "paperDoi": "10.1016/j.molcel.2010.06.024",
   "paperCite": "Gora KG et al. 2010 Mol Cell",
   "status": "live",
   "verified": "GEO GSE22062: 'sciP array data', taxid 190650, pubmed 20598601, 4 samples; summary describes CtrA and SciP."
  },
  {
   "id": "geo-gse46915",
   "name": "Cell-cycle RNA-seq, five stages (Fang 2013)",
   "category": "transcriptome",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "Deep RNA-seq of five cell-cycle stages (3 replicates each); 1,586 genes differentially expressed between stages.",
   "accession": "GSE46915",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46915",
   "paperDoi": "10.1186/1471-2164-14-450",
   "paperCite": "Fang G et al. 2013 BMC Genomics",
   "status": "live",
   "verified": "GEO GSE46915: 'Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution', RNA-seq, taxid 155892, pubmed 23829427, SRA SRP022592."
  },
  {
   "id": "geo-gse54883",
   "name": "Coding/noncoding genome architecture: RNA-seq, ribosome profiling, 5'-RACE (Schrader 2014)",
   "category": "transcriptome",
   "strain": "NA1000",
   "description": "Ribosome profiling, RNA-seq and global 5'-RACE used with LC-MS to redefine the coding potential of the NA1000 genome.",
   "accession": "GSE54883",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54883",
   "paperDoi": "10.1371/journal.pgen.1004463",
   "paperCite": "Schrader JM et al. 2014 PLoS Genet",
   "status": "live",
   "verified": "GEO GSE54883: 'The coding and noncoding architecture of the Caulobacter crescentus genome', taxid 565050, pubmed 25078267, 4 samples, SRA SRP037582."
  },
  {
   "id": "geo-gse157432",
   "name": "Genome-wide mRNA half-lives by rifampicin shutoff (Rif-seq)",
   "category": "transcriptome",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "mRNA decay measured 1-15 min after rifampicin in M2G mid-log cells, two biological replicate time courses.",
   "accession": "GSE157432",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157432",
   "paperDoi": "10.1016/j.celrep.2025.116691",
   "paperCite": "Dilrangi KH et al. 2025 Cell Rep",
   "status": "live",
   "verified": "GEO GSE157432: 'Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff', taxid 155892, pubmed 41391147 (Rif-seq paper), SRA SRP279989."
  },
  {
   "id": "geo-gse57366",
   "name": "Cell-cycle transcription start sites (Zhou 2015)",
   "category": "tss",
   "strain": "NA1000",
   "description": "SuperSeries (GSE57364 timecourse + GSE57365 mapping): modified global 5'-RACE mapped 2,726 TSS, 586 cell-cycle regulated.",
   "accession": "GSE57366",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57366",
   "paperDoi": "10.1371/journal.pgen.1004831",
   "paperCite": "Zhou B et al. 2015 PLoS Genet",
   "status": "live",
   "verified": "GEO GSE57366 'The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle', SuperSeries of GSE57364/GSE57365, taxid 565050, pubmed 25569173 (paper title 'The global regulatory architecture of transcription during the Caulobacter cell cycle'). Subseries SRA SRP041726/SRP041727."
  },
  {
   "id": "geo-gse68200",
   "name": "Cell-cycle ribosome profiling + RNA-seq (Schrader 2016)",
   "category": "translation",
   "strain": "NA1000",
   "description": "Ribosome profiling and RNA-seq across the cell cycle; translational control found in 51% of cell-cycle-regulated genes.",
   "accession": "GSE68200",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68200",
   "paperDoi": "10.1073/pnas.1614795113",
   "paperCite": "Schrader JM et al. 2016 PNAS",
   "status": "live",
   "verified": "GEO GSE68200: 'Ribosome Profiling Reveals Translational Control During the Caulobacter crescentus cell cycle', taxid 565050, pubmed 27791168 ('Dynamic translation regulation in Caulobacter cell cycle control'), SRA SRP057599."
  },
  {
   "id": "geo-gse126485",
   "name": "Absolute translation rates, ribosome profiling in M2G (Aretakis 2019)",
   "category": "translation",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "Ribosome profiling in M2G minimal medium to measure absolute mRNA translation levels.",
   "accession": "GSE126485",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126485",
   "paperDoi": "10.1128/mSystems.00170-19",
   "paperCite": "Aretakis JR et al. 2019 mSystems",
   "status": "live",
   "verified": "GEO GSE126485: 'Absolute measurements of mRNA translation in C. crescentus reveal important fitness costs of Vitamin B12 scavenging', taxid 155892, pubmed 31138672, SRA SRP185778."
  },
  {
   "id": "geo-gse52849",
   "name": "ChIP-seq of CtrA, SciP, MucR1/2, FlbD (Fumeaux 2014)",
   "category": "chip",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "ChIP-seq of CtrA, SciP, FlbD, MucR1, MucR2 (plus ΔpleC/ΔmucR12 controls) in Caulobacter, and orthologs in Sinorhizobium fredii; defines the S-to-G1 transcriptional switch.",
   "accession": "GSE52849",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52849",
   "paperDoi": "10.1038/ncomms5081",
   "paperCite": "Fumeaux C et al. 2014 Nat Commun",
   "status": "live",
   "verified": "GEO GSE52849: 'Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators', taxids 155892 + 380, pubmed 24939058; GSM titles CtrA_ChIPseq, SciP_ChIPseq, FlbD_ChIPseq, MucR1/2_ChIPseq."
  },
  {
   "id": "geo-gse73925",
   "name": "ChIP-seq of GcrA and RNA polymerase (Haakonsen 2015)",
   "category": "chip",
   "strain": "NA1000",
   "description": "ChIP-seq of GcrA-3xFLAG, RpoC, σ70 (RpoD), σ32 and σ54 (± rifampicin) showing GcrA acts as a σ70 cofactor at methylated promoters.",
   "accession": "GSE73925",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73925",
   "paperDoi": "10.1101/gad.270660.115",
   "paperCite": "Haakonsen DL et al. 2015 Genes Dev",
   "status": "live",
   "verified": "GEO GSE73925: 'The bacterial cell-cycle regulator GcrA is a σ70 co-factor that drives gene expression from a subset of methylated promoters.', taxid 155892, pubmed 26545812; GSM titles 'Laublab_NA1000_...'; paper cites GSE73925."
  },
  {
   "id": "geo-gse134017",
   "name": "CtrA ChIP-seq, exponential vs stationary phase (Delaby 2019)",
   "category": "chip",
   "strain": "NA1000",
   "description": "CtrA ChIP-seq in wild type and CtrA DNA-binding-domain mutants, plus ΔspoT/ΔptsP, in exponential and stationary phase.",
   "accession": "GSE134017",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134017",
   "paperDoi": "10.1093/nar/gkz846",
   "paperCite": "Delaby M et al. 2019 Nucleic Acids Res",
   "status": "live",
   "verified": "GEO GSE134017: 'Developmental switch within the bacterial cell cycle regulator CtrA', taxid 565050, pubmed 31598724 (paper: 'Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA'), SRA SRP213852."
  },
  {
   "id": "paper-fioravanti2013",
   "name": "GcrA ChIP-seq, WT vs ΔccrM (Fioravanti 2013)",
   "category": "chip",
   "strain": "NA1000",
   "description": "ChIP-seq of GcrA and of m6A marks in wild type and ΔccrM cells; GcrA binding depends on GANTC methylation. No GEO record found: results in supplementary Table S3.",
   "accession": null,
   "repository": "Supplementary (PLoS Genet)",
   "url": "https://doi.org/10.1371/journal.pgen.1003541",
   "paperDoi": "10.1371/journal.pgen.1003541",
   "paperCite": "Fioravanti A et al. 2013 PLoS Genet",
   "status": "live",
   "verified": "PMC3667746 full text: comparative ChIP-seq 'Analysis of the two data sets (Table S3)'; no GSE/SRA accession in text; not present in GEO Caulobacter series list (156 GSE)."
  },
  {
   "id": "geo-gse100233",
   "name": "ParB ChIP-seq on native and engineered parS sites (Tran 2018)",
   "category": "chip",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "ChIP-seq of ParB spreading around parS sites on the Caulobacter chromosome (some samples in E. coli).",
   "accession": "GSE100233",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100233",
   "paperDoi": "10.1093/nar/gkx1192",
   "paperCite": "Tran NT et al. 2018 Nucleic Acids Res",
   "status": "live",
   "verified": "GEO GSE100233: 'Permissive zones for the centromere-binding protein ParB on the Caulobacter crescentus chromosome', taxids 155892 + 562, pubmed 29186514, SRA SRP109788."
  },
  {
   "id": "geo-gse100657",
   "name": "GapR ChIP-seq and RNA-seq (Guo 2018)",
   "category": "chip",
   "strain": "NA1000",
   "description": "ChIP-seq and RNA-seq for GapR, a chromosome-structuring protein that binds overtwisted DNA and stimulates type II topoisomerases.",
   "accession": "GSE100657",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100657",
   "paperDoi": "10.1016/j.cell.2018.08.029",
   "paperCite": "Guo MS et al. 2018 Cell",
   "status": "live",
   "verified": "GEO GSE100657: 'A bacterial chromosome structuring protein binds overtwisted DNA to stimulate type II topoisomerases and enable DNA replication', taxid 565050, pubmed 30220456, SRA SRP110755."
  },
  {
   "id": "geo-gse45966",
   "name": "First bacterial Hi-C: Caulobacter chromosome organization (Le 2013)",
   "category": "chromosome-conformation",
   "strain": "NA1000 (GEO tag: CB15)",
   "description": "Hi-C of swarmer cells, drug treatments, smc and hup1/hup2 mutants and a synchronized cell-cycle time course; reveals chromosomal interaction domains.",
   "accession": "GSE45966",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45966",
   "paperDoi": "10.1126/science.1242059",
   "paperCite": "Le TB et al. 2013 Science",
   "status": "live",
   "verified": "GEO GSE45966: 'High-resolution mapping of the spatial organization of Caulobacter crescentus chromosome by chromosome conformation capture ... (Hi-C)', taxid 190650, pubmed 24158908, SRA SRP020913; all 23 GSM titles read 'Laublab_..._HiC_NA1000_...' although the organism field says CB15."
  },
  {
   "id": "geo-gse74364",
   "name": "Hi-C: transcription drives domain boundaries (Le & Laub 2016)",
   "category": "chromosome-conformation",
   "strain": "NA1000 (GEO tag: CB15)",
   "description": "Hi-C and RNA-seq showing transcription rate and transcript length set chromosomal interaction domain boundaries.",
   "accession": "GSE74364",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74364",
   "paperDoi": "10.15252/embj.201593561",
   "paperCite": "Le TB & Laub MT 2016 EMBO J",
   "status": "live",
   "verified": "GEO GSE74364: 'Transcription rate and transcript length drive the formation of chromosomal interaction domain...', taxid 190650, pubmed 27288403, SRA SRP065280."
  },
  {
   "id": "geo-gse97330",
   "name": "SMC ChIP-seq and Hi-C (Tran 2017)",
   "category": "chromosome-conformation",
   "strain": "CB15/NA1000 (GEO: species-level)",
   "description": "Hi-C and SMC ChIP-seq showing SMC progressively aligns chromosome arms from parS and is blocked by convergent transcription.",
   "accession": "GSE97330",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97330",
   "paperDoi": "10.1016/j.celrep.2017.08.026",
   "paperCite": "Tran NT et al. 2017 Cell Rep",
   "status": "live",
   "verified": "GEO GSE97330: 'SMC progressively aligns chromosomal arms in Caulobacter crescentus but is antagonized by convergent transcription', taxid 155892, pubmed 28854358, 57 samples, SRA SRP102929."
  },
  {
   "id": "paper-kozdon2013",
   "name": "PacBio SMRT methylome across the cell cycle (Kozdon 2013)",
   "category": "methylome",
   "strain": "NA1000",
   "description": "Base-resolution m6A/m5C methylome at five cell-cycle points; GANTC hemimethylation dynamics and new motifs. Results in SI Appendix; no GEO/SRA accession found.",
   "accession": null,
   "repository": "Supplementary (PNAS SI Appendix)",
   "url": "https://doi.org/10.1073/pnas.1319315110",
   "paperDoi": "10.1073/pnas.1319315110",
   "paperCite": "Kozdon JB et al. 2013 PNAS",
   "status": "live",
   "verified": "PubMed 24218615 is PNAS (not PLoS One as in the brief). PMC3845142 text cites only reference CP001340.1 and SI Appendix tables; elink pubmed->gds/sra/bioproject empty; SRA PacBio search for Caulobacter has no matching study."
  },
  {
   "id": "geo-gse79880",
   "name": "m6A methylome (SMRT) and MucR ChIP-exo across α-proteobacteria (Ardissone 2016)",
   "category": "methylome",
   "strain": "NA1000",
   "description": "Genome-wide m6A analyses in Caulobacter NA1000 and other bacteria showing conserved local hypomethylation, plus MucR1 ChIP-exo time course.",
   "accession": "GSE79880",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79880",
   "paperDoi": "10.1371/journal.pgen.1006499",
   "paperCite": "Ardissone S et al. 2016 PLoS Genet",
   "status": "live",
   "verified": "GEO GSE79880: 'Conserved local hypomethylation control during the bacterial cell cycle and by superimposed environmental cues', pubmed 27997543, sample taxids incl. 565050; SRA SRP072878 is a PacBio SMRT study."
  },
  {
   "id": "geo-gse260848",
   "name": "CcrM-dependent methylation by nanopore sequencing",
   "category": "methylome",
   "strain": "NA1000",
   "description": "Nanopore methylation profiling comparing CcrM-dependent m6A in Caulobacter NA1000 and Brucella abortus. No publication linked in GEO.",
   "accession": "GSE260848",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE260848",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "GEO GSE260848: 'Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing', Methylation profiling by HTS, taxids 565050 + 359391, no pubmed_id."
  },
  {
   "id": "paper-christen2011",
   "name": "Hyper-saturated Tn5 essential genome (Christen 2011)",
   "category": "fitness",
   "strain": "see paper",
   "description": "Tn-seq essential genome: 480 essential ORFs plus essential promoters, sRNAs and operons. Data are supplementary (Dataset 1, Excel); no SRA/GEO record found.",
   "accession": null,
   "repository": "Supplementary (Mol Syst Biol Dataset 1)",
   "url": "https://doi.org/10.1038/msb.2011.58",
   "paperDoi": "10.1038/msb.2011.58",
   "paperCite": "Christen B et al. 2011 Mol Syst Biol",
   "status": "live",
   "verified": "PMC3202797 full text: 'Dataset 1 Excel file containing several Supplemental data tables'; '480 essential ORFs'; elink pubmed->gds/sra/bioproject empty."
  },
  {
   "id": "fitness-browser-caulo",
   "name": "Fitness Browser: RB-TnSeq fitness data, orgId Caulo",
   "category": "fitness",
   "strain": "NA1000",
   "description": "Genome-wide mutant fitness (RB-TnSeq) across many conditions for C. crescentus NA1000 (CCNA_ locus tags), from Price et al. 2018 and later releases.",
   "accession": "Caulo",
   "repository": "Fitness Browser (LBNL)",
   "url": "https://fit.genomics.lbl.gov/cgi-bin/org.cgi?orgId=Caulo",
   "paperDoi": "10.1038/s41586-018-0124-0",
   "paperCite": "Price MN et al. 2018 Nature",
   "status": "live",
   "verified": "Site returns a bot-challenge (HTTP 403 'Just a moment...') to scripted requests, so page content could not be fetched. orgId verified in the July 2026 archive aaseqs.gz: 3,886 proteins with IDs 'Caulo:CCNA_xxxxx'; archive text says 'The current Fitness Browser is at http://fit.genomics.lbl.gov/'."
  },
  {
   "id": "figshare-fitness-browser-2026-07",
   "name": "Fitness Browser full data archive (July 2026)",
   "category": "fitness",
   "strain": "NA1000",
   "description": "Downloadable SQLite database, protein FASTA and per-strain fitness tables for all 62 Fitness Browser organisms, including Caulo.",
   "accession": "10.6084/m9.figshare.32865896",
   "repository": "figshare",
   "url": "https://doi.org/10.6084/m9.figshare.32865896",
   "paperDoi": "10.1038/s41586-018-0124-0",
   "paperCite": "Price MN et al. 2018 Nature",
   "status": "live",
   "verified": "figshare API article 32865896: 'Archive of the RB-TnSeq Fitness Browser, July 2026', files feba.db.gz, aaseqs.gz, StrainFitness.tar.gz, feba.tar.gz; downloaded aaseqs.gz and confirmed 'Caulo' entries."
  },
  {
   "id": "geo-gse119738",
   "name": "BarSeq adhesion screen (Hershey 2019)",
   "category": "fitness",
   "strain": "see paper (GEO: species-level)",
   "description": "Barcoded transposon (BarSeq) enrichment for mutants that fail to adhere to cheesecloth; genome-wide analysis of holdfast adhesion.",
   "accession": "GSE119738",
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119738",
   "paperDoi": "10.1128/mBio.02273-18",
   "paperCite": "Hershey DM et al. 2019 mBio",
   "status": "live",
   "verified": "GEO GSE119738: 'Barcoded DNA sequencing (BarSeq) samples from passaging of Caulobacter crescentus in medium containing cheesecloth', taxid 155892, pubmed 30755507, SRA SRP160994."
  },
  {
   "id": "paper-werner2009",
   "name": "Genome-scale protein localization screen (Werner 2009)",
   "category": "localization",
   "strain": "CB15 ORF library (host: see paper)",
   "description": "mCherry fusion libraries imaged at high throughput: 352 localized fusions, 289 unique proteins. Data in Table S1; the Gitai lab image site cited in the paper no longer responds.",
   "accession": null,
   "repository": "Supplementary (PNAS Table S1)",
   "url": "https://doi.org/10.1073/pnas.0901781106",
   "paperDoi": "10.1073/pnas.0901781106",
   "paperCite": "Werner JN et al. 2009 PNAS",
   "status": "live",
   "verified": "PMC2671984 text: 'results (Table S1), including images ... are accessible at the Gitai lab website: www.molbio1.princeton.edu/labs/gitai/' -> that URL 301s to mol-xray.princeton.edu, which gives no response (offline)."
  },
  {
   "id": "paper-iyerbiswas2014",
   "name": "Single-cell growth and division time-lapse (Iyer-Biswas 2014)",
   "category": "single-cell",
   "strain": "engineered adhesion-switchable strain (see paper)",
   "description": "~1,000 single stalked cells tracked for >100 generations each at controlled temperatures; exponential growth, division at ~1.8x initial size, universal scaling. Data in SI; no public repository accession found.",
   "accession": null,
   "repository": "Supplementary (PNAS SI)",
   "url": "https://doi.org/10.1073/pnas.1403232111",
   "paperDoi": "10.1073/pnas.1403232111",
   "paperCite": "Iyer-Biswas S et al. 2014 PNAS",
   "status": "live",
   "verified": "PubMed 25349411; PMC4234605 text points only to SI ('supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1403232111/-/DCSupplemental'); DataCite search for Iyer-Biswas returned no datasets. Text: 'measurement of ~1,000 single stalked cells for >100 generations each'."
  },
  {
   "id": "caulobrowser",
   "name": "CauloBrowser",
   "category": "database",
   "strain": "NA1000",
   "description": "Systems-biology portal integrating Caulobacter genome annotation, transcriptomics, ribosome profiling, localization and essentiality data.",
   "accession": null,
   "repository": "CauloBrowser",
   "url": "https://caulobrowser.org/",
   "paperDoi": "10.1093/nar/gkv1050",
   "paperCite": "Lasker K et al. 2016 Nucleic Acids Res",
   "status": "redirects",
   "verified": "caulobrowser.org (301 to https) now serves a ShinyProxy launcher at https://shinyproxy.gateway.harmony.unityhpc.org/app/caulobrowser (UMass Unity HPC); page title 'caulobrowser'. App content is JavaScript-launched and could not be confirmed loading from curl."
  },
  {
   "id": "uniprot-up000001364",
   "name": "UniProt reference proteome: NA1000",
   "category": "database",
   "strain": "NA1000",
   "description": "Reference proteome for 'Caulobacter vibrioides (strain NA1000 / CB15N)', 3,859 proteins, built on GCA_000022005.1.",
   "accession": "UP000001364",
   "repository": "UniProt",
   "url": "https://www.uniprot.org/proteomes/UP000001364",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "rest.uniprot.org proteomes organism_id:565050 -> UP000001364, Reference proteome, proteinCount 3859, assembly GCA_000022005.1. e.g. CtrA = B8H358 (CCNA_03130, reviewed)."
  },
  {
   "id": "uniprot-up000001816",
   "name": "UniProt reference proteome: CB15",
   "category": "database",
   "strain": "CB15",
   "description": "Reference proteome for 'Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)', 3,720 proteins.",
   "accession": "UP000001816",
   "repository": "UniProt",
   "url": "https://www.uniprot.org/proteomes/UP000001816",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "rest.uniprot.org proteomes organism_id:190650 -> UP000001816, Reference proteome, proteinCount 3720, assembly GCA_000006905.1. e.g. CtrA = P0CAW8 (CC_3035, reviewed)."
  },
  {
   "id": "kegg-ccs",
   "name": "KEGG organism ccs (NA1000)",
   "category": "database",
   "strain": "NA1000",
   "description": "KEGG genome T00841, 'Caulobacter vibrioides NA1000': pathways, modules and KO assignments for 3,886 proteins.",
   "accession": "ccs",
   "repository": "KEGG",
   "url": "https://www.kegg.jp/kegg-bin/show_organism?org=ccs",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "rest.kegg.jp/info/ccs -> 'ccs Caulobacter vibrioides NA1000, T00841, 3886 proteins, 1957 proteins with KOs'."
  },
  {
   "id": "kegg-ccr",
   "name": "KEGG organism ccr (CB15)",
   "category": "database",
   "strain": "CB15",
   "description": "KEGG genome T00049, 'Caulobacter vibrioides CB15': pathways, modules and KO assignments for 3,737 proteins.",
   "accession": "ccr",
   "repository": "KEGG",
   "url": "https://www.kegg.jp/kegg-bin/show_organism?org=ccr",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "rest.kegg.jp/info/ccr -> 'ccr Caulobacter vibrioides CB15, T00049, 3737 proteins, 1913 proteins with KOs'."
  },
  {
   "id": "biocyc-caulona1000",
   "name": "BioCyc CAULONA1000 (NA1000 pathway/genome database)",
   "category": "database",
   "strain": "NA1000",
   "description": "Tier 2 curated BioCyc PGDB for NA1000 (Stanford University, SRI International). BioCyc requires a free account/subscription for full access.",
   "accession": "CAULONA1000",
   "repository": "BioCyc",
   "url": "https://biocyc.org/organism-summary?object=CAULONA1000",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "biocyc.org/organism-summary?object=CAULONA1000 -> 'Summary of Caulobacter vibrioides NA1000, version 30.0', 'Tier 2 Curated Organism Database'; listed in biocyc-pgdb-list Tier 2."
  },
  {
   "id": "biocyc-caulo",
   "name": "BioCyc CAULO / CauloCyc (CB15 pathway/genome database)",
   "category": "database",
   "strain": "CB15",
   "description": "Tier 2 curated BioCyc PGDB for CB15 (SRI International, Stanford University).",
   "accession": "CAULO",
   "repository": "BioCyc",
   "url": "https://biocyc.org/organism-summary?object=CAULO",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "biocyc.org/organism-summary?object=CAULO -> 'Summary of Caulobacter vibrioides CB15 (CAULO), version 30.0', 'Tier 2 Curated Organism Database'."
  },
  {
   "id": "string-190650",
   "name": "STRING protein networks (CB15, taxid 190650)",
   "category": "database",
   "strain": "CB15",
   "description": "STRING v12.5 includes CB15 only (identifiers like 190650.CC_3035 for CtrA); NA1000 taxid 565050 is not in STRING.",
   "accession": "190650",
   "repository": "STRING",
   "url": "https://string-db.org/cgi/input?species=190650",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "STRING API get_string_ids ctrA species=190650 -> '190650.CC_3035', taxonName 'Caulobacter vibrioides CB15'; species=565050 -> 'unknown organism'; api/json/version -> 12.5."
  },
  {
   "id": "alphafold-db",
   "name": "AlphaFold DB predicted structures",
   "category": "structure",
   "strain": "NA1000 and CB15",
   "description": "Predicted models for UniProt proteins of both reference proteomes (e.g. CtrA: AF-B8H358-F1 for NA1000, AF-P0CAW8-F1 for CB15).",
   "accession": null,
   "repository": "AlphaFold DB",
   "url": "https://alphafold.ebi.ac.uk/entry/B8H358",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "alphafold.ebi.ac.uk/api/prediction/B8H358 -> AF-B8H358-F1, 'Caulobacter vibrioides (strain NA1000 / CB15N)', taxId 565050, v6; P0CAW8 -> AF-P0CAW8-F1, taxId 190650. No dedicated per-proteome download for Caulobacter was confirmed."
  },
  {
   "id": "rcsb-pdb-caulobacter",
   "name": "RCSB PDB: experimental structures from Caulobacter vibrioides",
   "category": "structure",
   "strain": "species (incl. CB15, NA1000)",
   "description": "Search of PDB entries whose source organism lineage includes taxid 155892 (209 entries on 2026-10-04: 74 tagged CB15, 49 NA1000).",
   "accession": null,
   "repository": "RCSB PDB",
   "url": "https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22rcsb_entity_source_organism.taxonomy_lineage.id%22%2C%22operator%22%3A%22exact_match%22%2C%22value%22%3A%22155892%22%7D%7D%2C%22return_type%22%3A%22entry%22%7D",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "search.rcsb.org v2 query taxonomy_lineage.id=155892 -> total_count 209 (190650 -> 74; 565050 -> 49; genus 75 -> 224). Count changes over time; the link runs the same query."
  },
  {
   "id": "paperblast",
   "name": "PaperBLAST (literature search by protein sequence)",
   "category": "database",
   "strain": "any",
   "description": "Finds papers about a protein or its homologs by sequence; includes curated Caulobacter literature. Same LBNL group as the Fitness Browser.",
   "accession": null,
   "repository": "PaperBLAST (LBNL)",
   "url": "https://papers.genomics.lbl.gov/cgi-bin/litSearch.cgi",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "Server responds HTTP 403 with a bot-challenge page ('Just a moment...') to scripted requests; content not verified by curl."
  },
  {
   "id": "microbesonline",
   "name": "MicrobesOnline genome page (NA1000)",
   "category": "database",
   "strain": "NA1000",
   "description": "Comparative genomics portal (operons, gene neighborhoods, expression). Taxonomy-id URL for NA1000.",
   "accession": "565050",
   "repository": "MicrobesOnline",
   "url": "http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=565050",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "URL redirects to https://microbesonline.org/... and returns a bot-check page ('Making sure you're not a bot!'); genome content not verified by curl. A tId=190650 (CB15) URL behaves the same."
  },
  {
   "id": "ensembl-bacteria-na1000",
   "name": "Ensembl Bacteria: NA1000 (archived)",
   "category": "database",
   "strain": "NA1000",
   "description": "Ensembl Bacteria genome page for 'Caulobacter vibrioides NA1000 (GCA_000022005)' (2022-12 Prokka genebuild, release 63). Ensembl Bacteria now serves it from an archive host.",
   "accession": "GCA_000022005",
   "repository": "Ensembl Bacteria",
   "url": "https://bacteria.ensembl.org/Caulobacter_vibrioides_na1000_gca_000022005/Info/Index",
   "paperDoi": null,
   "paperCite": null,
   "status": "redirects",
   "verified": "URL redirects to https://jun2026-bacteria.ensembl.org/Caulobacter_vibrioides_na1000_gca_000022005/Info/Index (page labelled 'Bacteria Archive'); bacteria.ensembl.org/index.html redirects to www.ensembl.org. REST info/genomes/taxonomy/565050 -> genebuild '2022-12-Prokka'. Archive host was flaky: one fetch 500, retry 200 (title '... - Ensembl Genomes 63')."
  },
  {
   "id": "geo-caulobacter-all",
   "name": "GEO: all Caulobacter series",
   "category": "database",
   "strain": "species",
   "description": "Search link for every GEO series with Caulobacter samples (156 series on 2026-10-04).",
   "accession": null,
   "repository": "GEO",
   "url": "https://www.ncbi.nlm.nih.gov/gds/?term=Caulobacter%5BOrganism%5D+AND+gse%5BEntry+Type%5D",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "E-utilities esearch db=gds 'Caulobacter[Organism] AND gse[Entry Type]' -> count 156."
  },
  {
   "id": "atcc-19089",
   "name": "ATCC 19089: strain CB15",
   "category": "strain",
   "strain": "CB15",
   "description": "Caulobacter vibrioides strain designation CB 15 [CIP 103742]; isolated from pond water; not the type strain. Genomic DNA sold as 19089D-5.",
   "accession": "ATCC 19089",
   "repository": "ATCC",
   "url": "https://www.atcc.org/products/19089",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "atcc.org/products/19089 title 'Caulobacter vibrioides Henrici and Johnson - 19089 | ATCC'; text: 'Strain designation CB 15 [CIP 103742] Type strain No Genome sequenced strain Yes Isolation source Pond water'; cites AE005673."
  },
  {
   "id": "bacdive-139101",
   "name": "BacDive 139101: CB15 (CIP 103742, ATCC 19089)",
   "category": "strain",
   "strain": "CB15",
   "description": "BacDive strain record for CB15; CB15 is held by ATCC and CIP but has no DSM number.",
   "accession": "139101",
   "repository": "BacDive (DSMZ)",
   "url": "https://bacdive.dsmz.de/strain/139101",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "bacdive.dsmz.de/strain/139101 title 'Caulobacter vibrioides CB 15 | CIP 103742, ATCC 19089 | BacDiveID:139101'. BacDive search for 'NA1000' -> 'Sorry, nothing found'."
  },
  {
   "id": "dsm-9893",
   "name": "DSM 9893: type strain CB51",
   "category": "strain",
   "strain": "CB51 (type strain)",
   "description": "Type strain of Caulobacter vibrioides (Stove CB51; KCTC 23677, CIP 106452, VKM B-1496). Distinct from CB15.",
   "accession": "DSM 9893",
   "repository": "DSMZ",
   "url": "https://www.dsmz.de/collection/catalogue/details/culture/DSM-9893",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "DSMZ catalogue DSM-9893: 'type strain ... Caulobacter vibrioides Strain designation: CB51 Other collection no.: KCTC 23677'."
  },
  {
   "id": "dsm-4727",
   "name": "DSM 4727: strain CB2 (former C. crescentus type strain)",
   "category": "strain",
   "strain": "CB2",
   "description": "Strain CB2 (ATCC 15252), isolated from tap water; type strain of the synonym C. crescentus.",
   "accession": "DSM 4727",
   "repository": "DSMZ",
   "url": "https://www.dsmz.de/collection/catalogue/details/culture/DSM-4727",
   "paperDoi": null,
   "paperCite": null,
   "status": "live",
   "verified": "DSMZ catalogue DSM-4727: 'Caulobacter vibrioides Strain designation: CB 2 Other collection no.: ATCC 15252 Isolated from: tap water'; LPSN lists CB2/ATCC 15252/DSM 4727 as C. crescentus type strain."
  },
  {
   "id": "addgene-laub-crispri",
   "name": "Addgene: Caulobacter CRISPRi plasmids (Laub lab)",
   "category": "plasmids",
   "strain": "see paper",
   "description": "14 plasmids: xylose/vanillate-inducible dCas9 (S. thermophilus, S. pasteurianus, S. pyogenes) and sgRNA vectors built on pXGFPC-5 / pBXMCS-2 / pVCERC-5 backbones.",
   "accession": null,
   "repository": "Addgene",
   "url": "https://www.addgene.org/search/catalog/plasmids/?q=Caulobacter",
   "paperDoi": "10.1128/mBio.02415-19",
   "paperCite": "Guzzo M et al. 2020 mBio",
   "status": "live",
   "verified": "Addgene catalog search 'Caulobacter' -> 44 results; 14 deposited by Michael Laub citing 'Guzzo et al mBio 2020', e.g. #133316-#133319, #133334, #133339-#133344."
  },
  {
   "id": "paper-thanbichler2007",
   "name": "Vanillate/xylose-inducible vector set (Thanbichler 2007)",
   "category": "plasmids",
   "strain": "CB15N (NA1000)",
   "description": "Widely used set of Caulobacter expression and integration vectors (pXMCS, pVMCS, pBXMCS, GFP/CFP/YFP/mCherry fusions). Not deposited at Addgene; paper says GenBank files are available on request.",
   "accession": null,
   "repository": "Paper (on request)",
   "url": "https://doi.org/10.1093/nar/gkm818",
   "paperDoi": "10.1093/nar/gkm818",
   "paperCite": "Thanbichler M et al. 2007 Nucleic Acids Res",
   "status": "live",
   "verified": "Addgene search 'Thanbichler' -> 1 unrelated result (pSR77, Randau lab); NCBI nuccore search for the vector names -> 0 hits; PMC2175322: 'Annotated sequence files in GenBank format are available for all vectors and may be obtained upon request.' Text names host strain CB15N."
  }
 ],
 "namingSource": "https://lpsn.dsmz.de/species/caulobacter-crescentus",
 "checked": "2026-10-04",
 "references": [
  {
   "doi": "10.1186/1471-2164-14-450",
   "pmid": "23829427",
   "cite": "Fang et al. 2013 BMC Genomics",
   "title": "Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution"
  },
  {
   "doi": "10.1016/j.celrep.2025.116691",
   "pmid": "41391147",
   "cite": "Dilrangi et al. 2025 Cell Reports",
   "title": "Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation"
  },
  {
   "doi": "10.1073/pnas.1614795113",
   "pmid": "27791168",
   "cite": "Schrader et al. 2016 Proc. Natl. Acad. Sci. U.S.A.",
   "title": "Dynamic translation regulation in Caulobacter cell cycle control"
  },
  {
   "doi": "10.1128/msystems.00170-19",
   "pmid": "31138672",
   "cite": "Aretakis et al. 2019 mSystems",
   "title": "Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B 12 Scavenging"
  },
  {
   "doi": "10.1101/gad.270660.115",
   "pmid": "26545812",
   "cite": "Haakonsen et al. 2015 Genes Dev.",
   "title": "The bacterial cell cycle regulator GcrA is a σ 70 cofactor that drives gene expression from a subset of methylated promoters"
  },
  {
   "doi": "10.1093/nar/gkz846",
   "pmid": "31598724",
   "cite": "Delaby et al. 2019 Nucleic Acids Research",
   "title": "Bacterial cell cycle and growth phase switch by the essential transcriptional regulator CtrA"
  },
  {
   "doi": "10.1371/journal.pgen.1003541",
   "pmid": "23737758",
   "cite": "Fioravanti et al. 2013 PLoS Genet",
   "title": "DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria"
  },
  {
   "doi": "10.1093/nar/gkx1192",
   "pmid": "29186514",
   "cite": "Tran et al. 2017 Nucleic Acids Research",
   "title": "Permissive zones for the centromere-binding protein ParB on the Caulobacter crescentus chromosome"
  },
  {
   "doi": "10.1016/j.cell.2018.08.029",
   "pmid": "30220456",
   "cite": "Guo et al. 2018 Cell",
   "title": "A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication"
  },
  {
   "doi": "10.15252/embj.201593561",
   "pmid": "27288403",
   "cite": "Le & Laub 2016 EMBO J",
   "title": "Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries"
  },
  {
   "doi": "10.1016/j.celrep.2017.08.026",
   "pmid": "28854358",
   "cite": "Tran et al. 2017 Cell Reports",
   "title": "SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription"
  },
  {
   "doi": "10.1371/journal.pgen.1006499",
   "pmid": "27997543",
   "cite": "Ardissone et al. 2016 PLoS Genet",
   "title": "Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria"
  },
  {
   "doi": "10.1128/mbio.02273-18",
   "pmid": "30755507",
   "cite": "Hershey et al. 2019 mBio",
   "title": "A Genome-Wide Analysis of Adhesion in Caulobacter crescentus Identifies New Regulatory and Biosynthetic Components for Holdfast Assembly"
  },
  {
   "doi": "10.1128/mbio.02415-19",
   "pmid": "31937638",
   "cite": "Guzzo et al. 2020 mBio",
   "title": "A CRISPR Interference System for Efficient and Rapid Gene Knockdown in Caulobacter crescentus"
  },
  {
   "doi": "10.1038/s41586-018-0124-0",
   "pmid": "29769716",
   "cite": "Price et al. 2018 Nature",
   "title": "Mutant phenotypes for thousands of bacterial genes of unknown function"
  }
 ]
}