{"database": "metadata", "table": "run_metadata", "rows": [[74913, "SRR24149995", "SRX19948131", "SRS17296333", "SRP432326", "PRJNA954890", "RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration", "GSE229567", "Other", "During development  multicellular rosettes serve as important cellular intermediates in the formation of diverse organ systems. Multicellular rosettes are transient epithelial structures that are defined by the apical constriction of cells towards the rosette center. Due to the important role these structures play during development  understanding the molecular mechanisms by which rosettes are formed and maintained is of high interest. Utilizing the zebrafish posterior lateral line primordium pLLP as a model system  we identify the RhoA GEF Mcf2lb as a regulator of rosette integrity. The pLLP is a group of 150 cells that migrates along the zebrafish trunk and is organized into epithelial rosettes; these are deposited along the trunk and will differentiate into sensory organs called neuromasts NMs. Using single cell RNA sequencing and whole mount in situ hybridization  we showed that mcf2lb is expressed in the pLLP during migration. Given the known role of RhoA in rosette formation  we asked whether Mcf2lb plays a role in regulating apical constriction of cells within rosettes. Live imaging and subsequent 3D analysis of mcf2lb mutant pLLP cells showed disrupted apical constriction and subsequent rosette organization. This in turn resulted in a unique posterior Lateral Line phenotype: an excess number of deposited NMs along the trunk of the zebrafish. Cell polarity markers ZO 1 and Par 3 were apically localized  indicating that pLLP cells are normally polarized. In contrast  signaling components that mediate apical constriction downstream of RhoA  Rock 2a and non muscle Myosin II were diminished apically. Altogether our results suggest a model whereby Mcf2lb activates RhoA  which in turn activates downstream signaling machinery to induce and maintain apical constriction in cells incorporated into rosettes. Overall design: Cells from Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of GFP and mCherry signal and analyzed using scRNAseq.", null, "pubmed:37131612;pubmed:38165177", null, "Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line  scRNAseq", "GSM7165622", null, "source name:zebrafish embryo|cell type:various|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line  scRNAseq", "using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", null, "30 hpf Tg 8.0claudinB:lynGFPzf106/ TgBACcxcr4b:F tractin mCherry zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer\u2019s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer\u2019s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:various|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7165622", "GSM7165622: Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line  scRNAseq; Danio rerio; RNA Seq", "GSM7165622 r1", "GSM7165622", "1", "30 hpf Tg 8.0claudinB:lynGFPzf106/ TgBACcxcr4b:F tractin mCherry zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28\u00b0 C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4\u00b0 C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4\u00b0 C for 5 minutes and supernatant was removed. 700 \u03bcl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u03bcm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 \u03bcl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP432326", null, "loader:fastq load.py", "CEL200317AN_zebrafish_pLLP_S2_L001_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S2_L001_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 4155084146.0, 32717198.0, "GSM7165622 r3", "0:8 1:28 2:91", "A:915445002;C:610150205;G:697623249;T:754003095;N:43467", 8, 28, 91, null, 915445002, 610150205, 697623249, 754003095, 43467, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.86488, null, 0.1772, null, 0.77053, null, 0.52905, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-04-12", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["74913"], "units": {}, "query_ms": 10.886766001931392}