{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[25127, "SRR25610724", "SRX21337840", "SRS18583009", "SRP454647", "PRJNA1004574", "Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf", "GSE240655", "Transcriptome Analysis", "Melanocytes of the skin have traditionally been viewed as a homogeneous population  however  recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further  we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study  we utilized a transgenic zebrafish line  Tgmifa:GFP  that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter  mitfa  labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer", "parent bioproject:PRJNA975369", "pubmed:39163475", null, "mitfa high  zf  scRNAseq", "GSM7706847", null, "tissue:mitfa:GFP+ cells|genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP high|age:24 hpf loc name:missing|collection date:missing", "mitfa high  zf  scRNAseq", "The demultiplexing  barcode processing  gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "mitfa:GFP+ cells", null, "Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5\u2005mg/ml pronase for 10 15\u2005min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100\u2005g for 2\u2005min at 4\u00b0C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30\u2005min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70\u2005\u03bcm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.", null, "genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP high|age:24 hpf", "GSM7706847", "GSM7706847: mitfa high  zf  scRNAseq; Danio rerio; RNA Seq", "GSM7706847 r1", "GSM7706847", "1", "Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5\u2005mg/ml pronase for 10 15\u2005min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100\u2005g for 2\u2005min at 4\u00b0C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30\u2005min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70\u2005\u03bcm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454647", null, "loader:fastq load.py", "HM_S4_L001_I1_001.fastq.gz HM_S4_L001_R1_001.fastq.gz HM_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 24842565758.0, 195610754.0, "GSM7706847 r1", "0:8 1:28 2:91", "A:5175410152;C:3650416721;G:4658958024;T:4315769305;N:24412", 8, 28, 91, null, 5175410152, 3650416721, 4658958024, 4315769305, 24412, "SRX21337840", "SRS18583009", "SRA1691286", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", 1, 0.84133, null, 0.13672, null, 0.84756, null, 0.52135, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "India", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25128, "SRR25610725", "SRX21337839", "SRS18583008", "SRP454647", "PRJNA1004574", "Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf", "GSE240655", "Transcriptome Analysis", "Melanocytes of the skin have traditionally been viewed as a homogeneous population  however  recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further  we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study  we utilized a transgenic zebrafish line  Tgmifa:GFP  that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter  mitfa  labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer", "parent bioproject:PRJNA975369", "pubmed:39163475", null, "mitfa low  zf  scRNAseq", "GSM7706846", null, "tissue:mitfa:GFP+ cells|genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf loc name:missing|collection date:missing", "mitfa low  zf  scRNAseq", "The demultiplexing  barcode processing  gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "mitfa:GFP+ cells", null, "Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5\u2005mg/ml pronase for 10 15\u2005min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100\u2005g for 2\u2005min at 4\u00b0C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30\u2005min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70\u2005\u03bcm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter\u2019s instructions single cell 3\u2019 v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.", null, "genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf", "GSM7706846", "GSM7706846: mitfa low  zf  scRNAseq; Danio rerio; RNA Seq", "GSM7706846 r1", "GSM7706846", "1", "Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5\u2005mg/ml pronase for 10 15\u2005min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100\u2005g for 2\u2005min at 4\u00b0C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30\u2005min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70\u2005\u03bcm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454647", null, "loader:fastq load.py", "LM_S3_L001_R2_001.fastq.gz LM_S3_L001_R1_001.fastq.gz LM_S3_L001_I1_001.fastq.gz", "fastq fastq fastq", 17519211850.0, 137946550.0, "GSM7706846 r1", "0:8 1:28 2:91", "A:3674575574;C:2564940740;G:3313017210;T:3000585838;N:16688", 8, 28, 91, null, 3674575574, 2564940740, 3313017210, 3000585838, 16688, "SRX21337839", "SRS18583008", "SRA1691286", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", 1, 0.81163, null, 0.13698, null, 0.859, null, 0.52032, null, 91, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "India", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25129, "SRR25619749", "SRX21346683", "SRS18591743", "SRP454714", "PRJNA1004663", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival", "GSE240721", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "GSM7708237", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7708237", "GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq", "GSM7708237 r1", "GSM7708237", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454714", null, "loader:fastq load.py", "CEL201106AN_WT-2_S20_L004_R2_001.fastq.gz CEL201106AN_WT-2_S20_L004_R1_001.fastq.gz CEL201106AN_WT-2_S20_L004_I1_001.fastq.gz", "fastq fastq fastq", 17931740743.0, 141194809.0, "GSM7708237 r1", "0:8 1:28 2:91", "A:3982504087;C:2545259636;G:2793618614;T:3526744725;N:600557", 8, 28, 91, null, 3982504087, 2545259636, 2793618614, 3526744725, 600557, "SRX21346683", "SRS18591743", "SRA1691311", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.87401, null, 0.26924, null, 0.7517, null, 0.5102, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25130, "SRR25619750", "SRX21346683", "SRS18591743", "SRP454714", "PRJNA1004663", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival", "GSE240721", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "GSM7708237", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7708237", "GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq", "GSM7708237 r1", "GSM7708237", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454714", null, "loader:fastq load.py", "CEL201106AN_WT-2_S19_L004_I1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R2_001.fastq.gz", "fastq fastq fastq", 15740158766.0, 123938258.0, "GSM7708237 r2", "0:8 1:28 2:91", "A:3499017196;C:2231848518;G:2450171440;T:3096822046;N:522278", 8, 28, 91, null, 3499017196, 2231848518, 2450171440, 3096822046, 522278, "SRX21346683", "SRS18591743", "SRA1691311", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.87457, null, 0.27073, null, 0.75278, null, 0.50801, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25131, "SRR25619751", "SRX21346683", "SRS18591743", "SRP454714", "PRJNA1004663", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival", "GSE240721", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "GSM7708237", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7708237", "GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq", "GSM7708237 r1", "GSM7708237", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454714", null, "loader:fastq load.py", "CEL201106AN_WT-2_S18_L004_R2_001.fastq.gz CEL201106AN_WT-2_S18_L004_R1_001.fastq.gz CEL201106AN_WT-2_S18_L004_I1_001.fastq.gz", "fastq fastq fastq", 14146022254.0, 111386002.0, "GSM7708237 r3", "0:8 1:28 2:91", "A:3147384451;C:2003642594;G:2200506573;T:2784120122;N:472442", 8, 28, 91, null, 3147384451, 2003642594, 2200506573, 2784120122, 472442, "SRX21346683", "SRS18591743", "SRA1691311", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.873, null, 0.27005, null, 0.75122, null, 0.5172, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25132, "SRR25619752", "SRX21346683", "SRS18591743", "SRP454714", "PRJNA1004663", "Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival", "GSE240721", "Other", "Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq", "GSM7708237", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM7708237", "GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq", "GSM7708237 r1", "GSM7708237", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP454714", null, "loader:fastq load.py", "CEL201106AN_WT-2_S17_L004_I1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R2_001.fastq.gz", "fastq fastq fastq", 14874414752.0, 117121376.0, "GSM7708237 r4", "0:8 1:28 2:91", "A:3301539475;C:2111151786;G:2317995421;T:2926865071;N:493463", 8, 28, 91, null, 3301539475, 2111151786, 2317995421, 2926865071, 493463, "SRX21346683", "SRS18591743", "SRA1691311", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.87465, null, 0.26977, null, 0.75211, null, 0.51651, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-08-11", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31872, "SRR28764740", "SRX24330059", "SRS21091017", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 48h", "GSM8222580", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf loc name:missing|collection date:missing", "CEL210312AN WT 48h", "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, "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf", "GSM8222580", "GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq", "GSM8222580 r1", "GSM8222580", "1", "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_48h_S100_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S100_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S100_L003_R2_001.fastq.gz", "fastq fastq fastq", 8597674702.0, 67698226.0, "GSM8222580 r1", "0:8 1:28 2:91", "A:1824246454;C:1278127991;G:1448333280;T:1609791598;N:39243", 8, 28, 91, null, 1824246454, 1278127991, 1448333280, 1609791598, 39243, "SRX24330059", "SRS21091017", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31873, "SRR28764741", "SRX24330059", "SRS21091017", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 48h", "GSM8222580", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf loc name:missing|collection date:missing", "CEL210312AN WT 48h", "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, "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf", "GSM8222580", "GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq", "GSM8222580 r1", "GSM8222580", "1", "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_48h_S101_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S101_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S101_L003_R2_001.fastq.gz", "fastq fastq fastq", 10521686856.0, 82847928.0, "GSM8222580 r2", "0:8 1:28 2:91", "A:2230570510;C:1564859730;G:1774018840;T:1969664072;N:48296", 8, 28, 91, null, 2230570510, 1564859730, 1774018840, 1969664072, 48296, "SRX24330059", "SRS21091017", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31874, "SRR28764742", "SRX24330059", "SRS21091017", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 48h", "GSM8222580", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf loc name:missing|collection date:missing", "CEL210312AN WT 48h", "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, "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf", "GSM8222580", "GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq", "GSM8222580 r1", "GSM8222580", "1", "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_48h_S102_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S102_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S102_L003_R2_001.fastq.gz", "fastq fastq fastq", 10393048429.0, 81835027.0, "GSM8222580 r3", "0:8 1:28 2:91", "A:2205422432;C:1544223539;G:1750760277;T:1946533138;N:48071", 8, 28, 91, null, 2205422432, 1544223539, 1750760277, 1946533138, 48071, "SRX24330059", "SRS21091017", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31875, "SRR28764743", "SRX24330059", "SRS21091017", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 48h", "GSM8222580", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf loc name:missing|collection date:missing", "CEL210312AN WT 48h", "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, "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:48 hpf", "GSM8222580", "GSM8222580: CEL210312AN WT 48h; Danio rerio; RNA Seq", "GSM8222580 r1", "GSM8222580", "1", "Forty eight hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_48h_S103_L003_I1_001.fastq.gz CEL210312AN_WT_48h_S103_L003_R1_001.fastq.gz CEL210312AN_WT_48h_S103_L003_R2_001.fastq.gz", "fastq fastq fastq", 1539235301.0, 12119963.0, "GSM8222580 r4", "0:8 1:28 2:91", "A:326058980;C:228846142;G:262343444;T:285660694;N:7373", 8, 28, 91, null, 326058980, 228846142, 262343444, 285660694, 7373, "SRX24330059", "SRS21091017", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31876, "SRR28764744", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "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, "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S96_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S96_L003_R2_001.fastq.gz", "fastq fastq fastq", 9045377769.0, 71223447.0, "GSM8222579 r1", "0:8 1:28 2:91", "A:1910521348;C:1357874019;G:1521970464;T:1690926373;N:41473", 8, 28, 91, null, 1910521348, 1357874019, 1521970464, 1690926373, 41473, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31877, "SRR28764745", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "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, "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S97_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S97_L003_R2_001.fastq.gz", "fastq fastq fastq", 9556753429.0, 75250027.0, "GSM8222579 r2", "0:8 1:28 2:91", "A:2016694527;C:1436202913;G:1608693558;T:1786117733;N:43726", 8, 28, 91, null, 2016694527, 1436202913, 1608693558, 1786117733, 43726, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31878, "SRR28764746", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "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, "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S98_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S98_L003_R2_001.fastq.gz", "fastq fastq fastq", 6838295188.0, 53844844.0, "GSM8222579 r3", "0:8 1:28 2:91", "A:1443225941;C:1028068269;G:1151922277;T:1276632644;N:31673", 8, 28, 91, null, 1443225941, 1028068269, 1151922277, 1276632644, 31673, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31879, "SRR28764747", "SRX24330058", "SRS21091016", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 22h", "GSM8222579", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf loc name:missing|collection date:missing", "CEL210312AN WT 22h", "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, "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:22 hpf", "GSM8222579", "GSM8222579: CEL210312AN WT 22h; Danio rerio; RNA Seq", "GSM8222579 r1", "GSM8222579", "1", "Twenty two hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_22h_S99_L003_I1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R1_001.fastq.gz CEL210312AN_WT_22h_S99_L003_R2_001.fastq.gz", "fastq fastq fastq", 8872634401.0, 69863263.0, "GSM8222579 r4", "0:8 1:28 2:91", "A:1873119195;C:1332238982;G:1493221194;T:1658936897;N:40665", 8, 28, 91, null, 1873119195, 1332238982, 1493221194, 1658936897, 40665, "SRX24330058", "SRS21091016", "SRA1850361", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31880, "SRR28738013", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "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, "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S92_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S92_L003_R2_001.fastq.gz", "fastq fastq fastq", 5909782440.0, 46533720.0, "GSM8216056 r1", "0:8 1:28 2:91", "A:1195361841;C:933687818;G:1057254177;T:1048237872;N:26812", 8, 28, 91, null, 1195361841, 933687818, 1057254177, 1048237872, 26812, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31881, "SRR28738014", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "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, "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S93_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S93_L003_R2_001.fastq.gz", "fastq fastq fastq", 6519796333.0, 51336979.0, "GSM8216056 r2", "0:8 1:28 2:91", "A:1320007258;C:1029906863;G:1166350676;T:1155370144;N:30148", 8, 28, 91, null, 1320007258, 1029906863, 1166350676, 1155370144, 30148, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31882, "SRR28738015", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "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, "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S94_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S94_L003_R2_001.fastq.gz", "fastq fastq fastq", 6288014983.0, 49511929.0, "GSM8216056 r3", "0:8 1:28 2:91", "A:1273032152;C:992961980;G:1124384567;T:1115177910;N:28930", 8, 28, 91, null, 1273032152, 992961980, 1124384567, 1115177910, 28930, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31883, "SRR28738016", "SRX24303940", "SRS21066774", "SRP502657", "PRJNA1101966", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling", "GSE264323", "Transcriptome Analysis", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Fourteen hpf  eighteen hpf  twenty two hpf  forty eight hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "CEL210312AN WT 14h", "GSM8216056", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf loc name:missing|collection date:missing", "CEL210312AN WT 14h", "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, "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:14 hpf", "GSM8216056", "GSM8216056: CEL210312AN WT 14h; Danio rerio; RNA Seq", "GSM8216056 r1", "GSM8216056", "1", "Fourteen hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP502657", null, "loader:fastq load.py", "CEL210312AN_WT_14h_S95_L003_I1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R1_001.fastq.gz CEL210312AN_WT_14h_S95_L003_R2_001.fastq.gz", "fastq fastq fastq", 6986621409.0, 55012767.0, "GSM8216056 r4", "0:8 1:28 2:91", "A:1412426673;C:1104618149;G:1250890162;T:1238194657;N:32156", 8, 28, 91, null, 1412426673, 1104618149, 1250890162, 1238194657, 32156, "SRX24303940", "SRS21066774", "SRA1848682", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-18", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31972, "SRR28854385", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S4_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 5724917176.0, 45078088.0, "GSM8244692 r1", "0:8 1:28 2:91", "A:1233470398;C:840754101;G:925102747;T:1102656199;N:122563", 8, 28, 91, null, 1233470398, 840754101, 925102747, 1102656199, 122563, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31973, "SRR28854386", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S4_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 5783895468.0, 45542484.0, "GSM8244692 r2", "0:8 1:28 2:91", "A:1245735118;C:849017838;G:935656364;T:1113856043;N:100681", 8, 28, 91, null, 1245735118, 849017838, 935656364, 1113856043, 100681, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31974, "SRR28854387", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S3_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 6548658861.0, 51564243.0, "GSM8244692 r3", "0:8 1:28 2:91", "A:1411724640;C:961558289;G:1057832581;T:1261091330;N:139273", 8, 28, 91, null, 1411724640, 961558289, 1057832581, 1261091330, 139273, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31975, "SRR28854388", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S3_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 6602135640.0, 51985320.0, "GSM8244692 r4", "0:8 1:28 2:91", "A:1422617276;C:968975306;G:1067723068;T:1271232295;N:116175", 8, 28, 91, null, 1422617276, 968975306, 1067723068, 1271232295, 116175, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31976, "SRR28854389", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S2_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 5207105156.0, 41000828.0, "GSM8244692 r5", "0:8 1:28 2:91", "A:1121297258;C:765571677;G:841433529;T:1002663097;N:109787", 8, 28, 91, null, 1121297258, 765571677, 841433529, 1002663097, 109787, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31977, "SRR28854390", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S2_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 5257051208.0, 41394104.0, "GSM8244692 r6", "0:8 1:28 2:91", "A:1131659183;C:772616863;G:850242289;T:1012253749;N:91380", 8, 28, 91, null, 1131659183, 772616863, 850242289, 1012253749, 91380, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31978, "SRR28854391", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S1_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 5671346544.0, 44656272.0, "GSM8244692 r7", "0:8 1:28 2:91", "A:1221772454;C:832992882;G:915744544;T:1093089728;N:121144", 8, 28, 91, null, 1221772454, 832992882, 915744544, 1093089728, 121144, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [31979, "SRR28854392", "SRX24414680", "SRS21169984", "SRP505049", "PRJNA1106549", "Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h", "GSE266312", "Other", "During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas \u201cpioneer\u201d is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 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 \u00b5l of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 \u00b5m 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 \u00b5l PBS/ 2% BSA in a siliconized 1.5mL tube.", null, null, null, "scRNAseq", "GSM8244692", null, "source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing", "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, "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter\u2019s instructions single cell 3\u2019 v3 protocol  10x Genomics.", null, "cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf", "GSM8244692", "GSM8244692: scRNAseq; Danio rerio; RNA Seq", "GSM8244692 r1", "GSM8244692", "1", "Thirty hpf TgBACneurod1:EGFPnl1 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 manufacter's instructions single cell three prime v3 protocol  10x Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP505049", null, "loader:fastq load.py", "CEL200616AN_WT_30h_S1_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 5728522071.0, 45106473.0, "GSM8244692 r8", "0:8 1:28 2:91", "A:1233691562;C:840924973;G:926085790;T:1103887111;N:99607", 8, 28, 91, null, 1233691562, 840924973, 926085790, 1103887111, 99607, "SRX24414680", "SRS21169984", "SRA1856329", "Oregon Health and Science Univ", "Oregon Health and Science Univ", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-04-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33008, "SRR29632270", "SRX25138332", "SRS21830414", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 24h", "GSM8366755", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 24h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366755", "GSM8366755: Bmp4 explant 24h; Danio rerio; RNA Seq", "GSM8366755 r1", "GSM8366755", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_24h_S1_L001_R1_001.fastq.gz Bmp4_24h_S1_L001_R2_001.fastq.gz", "fastq fastq", 49098784294.0, 412594826.0, "GSM8366755 r1", "0:28 1:91", "A:13643133254;C:11126085942;G:11676909916;T:12651522663;N:1132519", 28, 91, null, null, 13643133254, 11126085942, 11676909916, 12651522663, 1132519, "SRX25138332", "SRS21830414", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33009, "SRR29632271", "SRX25138331", "SRS21830413", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 18h", "GSM8366754", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 18h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366754", "GSM8366754: Bmp4 explant 18h; Danio rerio; RNA Seq", "GSM8366754 r1", "GSM8366754", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_18h_S1_L001_R1_001.fastq.gz Bmp4_18h_S1_L001_R2_001.fastq.gz", "fastq fastq", 44863080801.0, 377000679.0, "GSM8366754 r1", "0:28 1:91", "A:12441486571;C:10199111519;G:10790306255;T:11430847129;N:1329327", 28, 91, null, null, 12441486571, 10199111519, 10790306255, 11430847129, 1329327, "SRX25138331", "SRS21830413", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33010, "SRR29632272", "SRX25138330", "SRS21830412", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 12h", "GSM8366753", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 12h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366753", "GSM8366753: Bmp4 explant 12h; Danio rerio; RNA Seq", "GSM8366753 r1", "GSM8366753", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_12h_S1_L001_R1_001.fastq.gz Bmp4_12h_S1_L001_R2_001.fastq.gz", "fastq fastq", 50138128747.0, 421328813.0, "GSM8366753 r1", "0:28 1:91", "A:14089229753;C:10936347905;G:11403388741;T:13708020723;N:1141625", 28, 91, null, null, 14089229753, 10936347905, 11403388741, 13708020723, 1141625, "SRX25138330", "SRS21830412", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33011, "SRR29632273", "SRX25138329", "SRS21830410", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 10h", "GSM8366752", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 10h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366752", "GSM8366752: Bmp4 explant 10h; Danio rerio; RNA Seq", "GSM8366752 r1", "GSM8366752", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4-10h_S1_L001_R1_001.fastq.gz Bmp4-10h_S1_L001_R2_001.fastq.gz", "fastq fastq", 149164547700.0, 497215159.0, "GSM8366752 r1", "0:150 1:150", "A:44020073879;C:31344780625;G:29505876494;T:44289819189;N:3997513", 150, 150, null, null, 44020073879, 31344780625, 29505876494, 44289819189, 3997513, "SRX25138329", "SRS21830410", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33012, "SRR29632274", "SRX25138328", "SRS21830409", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 8h", "GSM8366751", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 8h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366751", "GSM8366751: Bmp4 explant 8h; Danio rerio; RNA Seq", "GSM8366751 r1", "GSM8366751", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4-8h_S1_L001_R1_001.fastq.gz Bmp4-8h_S1_L001_R2_001.fastq.gz", "fastq fastq", 118709118600.0, 395697062.0, "GSM8366751 r1", "0:150 1:150", "A:35474636770;C:23305712896;G:22894585568;T:37031410017;N:2773349", 150, 150, null, null, 35474636770, 23305712896, 22894585568, 37031410017, 2773349, "SRX25138328", "SRS21830409", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33013, "SRR29632275", "SRX25138327", "SRS21830411", "SRP516621", "PRJNA1129168", "in vitro construction of an embryonic caudal organizer", "GSE270989", "Other", "Purpose: Characterization of cell types in bmp4 explants and BMP4 induced human embryoids. Methods:  Single cell transcriptomes of bmp4 explants were harvested at 6 hpf  8 hpf 10 hpf  12 hpf  18 hpf and 24 hpf. Single cell transcriptomes of BMP4 induced human embryoids were harvested at Day 5 and Day 6. Libraries were prepared using Single Cell three primeLibrary & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery. Results: paraxial mesoderm  lateral plate mesoderm  and their derivatives were detected in bmp4 explants  and NMP  somite and neural cell fates were detected in bmp4 induced human embryoids. Conclusions: A well organized caudal like structure was induced in bmp4 explants and caudal cell fates were specified in BMP4 induced human embryoids. Overall design: bmp4 injected zebrafish explants or BMP4 induced human embryoids  were harvested  for scRNA seq.", null, null, null, "Bmp4 explant 6h", "GSM8366750", null, "source name:embryonic|tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell|geo loc name:missing|collection date:missing", "Bmp4 explant 6h", "Illumina sequencing reads were aligned to the zebrafish GRCz11 or human mRNA reference genome GRCh38 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11  GRCh38 Supplementary files format and content: tar archive includes filtered gene bc matrices post running CellRanger pipeline", "embryonic", "To generate bmp4 explants  bmp4 8 10 pg mRNA was injected into one animal pole blastomere at the 128 cell stage. Then the animal pole region was explanted and raised to 24hpf. To generate BMP4 induced human embryoids  human embryonic stem cells hESCs of the H9 line were grown on Matrigel coated 12 well plates for a period ranging from 48 to 72 hours  utilizing them when they reached an approximate confluence of 70%. On the initial day of the experiment  both wild type H9 cells and ihBmp4 cells were treated with accutase to facilitate their dissociation. They were then transferred to 96 well U bottom low attachment plates for culture. The seeding density was adjusted to 1300 cells per well for H9 cells and 400 cells per well for ihBmp4 cells  using 50 \u03bcl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10\u03bcM Y27632. post a 24 hour incubation period  both types of cells formed embryoid bodies EBs in their respective wells. These H9 and ihBmp4 EBs were then co cultured in the same well  with 80 \u03bcl of the TeSR E6 based medium to encourage fusion. Between days 2 and 4 of the culture period  the EBs were subjected to an induction process to enhance Bmp4 expression  which initiated the morphogenesis phase. The culture medium was replaced with a fresh TeSR E6 medium that included 75 ng ml 1 Doxycycline and 50 ng ml 1 FGF2 to stimulate these processes. Starting from day 4  the Doxycycline and FGF2 were omitted from the culture medium. The EBs were then maintained in a TeSR E6 based medium for continued growth and development.", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer\u2019s protocol for 10000 cell recovery.", "Bmp4 explants were cultured in Dulbecco's modified Eagle\u2019s medium DMEM/F 12 with 10 mM HEPES  1x MEM with non essential amino acids  7 mM CaCl2  1 mM sodium pyruvate  50 \u03bcg/ml gentamycin  100 \u03bcM 2 mercaptoethanol  1\u00d7 antibiotic antimycotic  10% serum replacement and kept at 28.5\u2103.BMP4 induced human embryoids were cultured in a 96 well U shaped ultra low plate with culture medium TeSR E6 medium supplemented with 0.5% N2 and 0.5% B27 to support cell growth. Small molecule compounds and recombinant proteins inducing differentiation were added according to the treatment protocol. Samples were collected on day 5 and 6 of differentiation.", "tissue:embryonic|cell line:zebrafish embryonic stem cells|cell type:stem cell", "GSM8366750", "GSM8366750: Bmp4 explant 6h; Danio rerio; RNA Seq", "GSM8366750 r1", "GSM8366750", "1", "Single cell RNA of each sample was extracted by following the Chromium Controller and Chromium Single Cell 30 Library & Gel Bead Kit  v3.110x Genomics  PN 1000121 protocol. Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3.1 10x Genomics  Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP516621", null, null, "Bmp4_6h_S1_L001_R1_001.fastq.gz Bmp4_6h_S1_L001_R2_001.fastq.gz", "fastq fastq", 52586645972.0, 441904588.0, "GSM8366750 r1", "0:28 1:91", "A:14755432217;C:11271293276;G:11858476334;T:14700289448;N:1154697", 28, 91, null, null, 14755432217, 11271293276, 11858476334, 14700289448, 1154697, "SRX25138327", "SRS21830411", "SRA1911917", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-06-27", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33617, "SRR30274406", "SRX25735496", "SRS22375280", "SRP526857", "PRJNA1148965", "The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development", "GSE275013", "Transcriptome Analysis", "Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes  but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question  we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 /  embryos. Loss of Gq/11 activity fully recapitulated the edn1 /  phenotype  with genes encoding for G11 being most essential. Furthermore  inducing Gq activity in edn1 /  embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16   36 hpf. Then  cranial neural crest cells NCCs labeled with two transgenes  sox10:mRFP and fli1a:EGFP  were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.", null, "pubmed:39345358;pubmed:40171762", null, "cranial NCCs  YM", "GSM8464445", null, "source name:Facial mesenchyme|tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM|geo loc name:missing|collection date:missing", "cranial NCCs  YM", "Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Facial mesenchyme", "Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer\u2019s solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz\u2019s L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM", "GSM8464445", "GSM8464445: cranial NCCs  YM; Danio rerio; RNA Seq", "GSM8464445 r1", "GSM8464445", "1", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz's L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP526857", null, null, "YM-treated_S9_L001_R2_001.fastq.gz YM-treated_S9_L001_R1_001.fastq.gz", "fastq fastq", 133560759038.0, 442254169.0, "GSM8464445 r1", "0:151 1:151", "A:49523643076;C:22144256343;G:30982866215;T:30893839980;N:16153424", 151, 151, null, null, 49523643076, 22144256343, 30982866215, 30893839980, 16153424, "SRX25735496", "SRS22375280", "SRA1949431", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", 2, 0.00156, 0.3917, 0.00133, 0.06002, 0.99997, 0.9529, 0.0, 0.52259, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-16", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33618, "SRR30274407", "SRX25735495", "SRS22375277", "SRP526857", "PRJNA1148965", "The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development", "GSE275013", "Transcriptome Analysis", "Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes  but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question  we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 /  embryos. Loss of Gq/11 activity fully recapitulated the edn1 /  phenotype  with genes encoding for G11 being most essential. Furthermore  inducing Gq activity in edn1 /  embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16   36 hpf. Then  cranial neural crest cells NCCs labeled with two transgenes  sox10:mRFP and fli1a:EGFP  were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.", null, "pubmed:39345358;pubmed:40171762", null, "cranial NCCs  DMSO", "GSM8464444", null, "source name:Facial mesenchyme|tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:DMSO|geo loc name:missing|collection date:missing", "cranial NCCs  DMSO", "Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "Facial mesenchyme", "Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer\u2019s solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz\u2019s L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:DMSO", "GSM8464444", "GSM8464444: cranial NCCs  DMSO; Danio rerio; RNA Seq", "GSM8464444 r1", "GSM8464444", "1", "Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4\u02daC with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz's L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP526857", null, null, "untreated_S8_L001_R2_001.fastq.gz untreated_S8_L001_R1_001.fastq.gz", "fastq fastq", 105068673228.0, 347909514.0, "GSM8464444 r1", "0:151 1:151", "A:37833743112;C:17968955370;G:25241339852;T:24012078661;N:12556233", 151, 151, null, null, 37833743112, 17968955370, 25241339852, 24012078661, 12556233, "SRX25735495", "SRS22375277", "SRA1949431", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", "David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus", 2, 0.00043, 0.49133, 0.00042, 0.07262, 1.0, 0.95179, null, 0.5212, 151, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-16", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [35979, "SRR33380663", "SRX28623695", "SRS24895016", "SRP582260", "PRJNA1256738", "Angptl5 restricts primitive hematopoiesis by modulating retinoic acid signaling in zebrafish", "GSE295891", "Other", "Purpose: Characterization of cell types in angptl5?10/?10 zebrafish. Methods: The angptl5?10/?10 embryos were raised in 0.3\u00d7 Danieau Buffer and harvested at 16 hpf. Collected samples were digested with trypsin into single cell suspension for single cell sequencing. Libraries were constructed with  a Chromium Single Cell three primev3 Reagent Kit 10x Genomics according to the manufacturer's protocol for 7350 cell recovery.Sequencing was performed with Illumina Novaseq 6000 according to the manufacturer's instructions Illumina. Results:  Global amplification of myeloid and erythroid progenitors in angptl5?10/?10 embryos. Conclusions: Angptl5 regulated primitive hematopoiesis in zebrafish. Overall design: Collected samples of angptl5?10/?10 embryos at 16 hpf were digested with trypsin into single cell suspension for  scRNA seq.", null, null, null, "A5 /  16 hpf", "GSM8960245", null, "source name:embryonic cells|tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h|geo loc name:missing|collection date:missing", "A5 /  16 hpf", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed  files include filtered gene bc matrices post running CellRanger pipeline", "embryonic cells", "Collected samples were digested with trypsin into single cell suspension and set to Novogene for single cell sequencing.", "RNA from the barcoded cells was reverse transcribed  reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3 10x Genomics  Cat# PN 1000268 according to the manufacturer\u2019s protocol for 7350 cell recovery.", "The angptl5\u039410/\u039410 embryos were raised in 0.3\u00d7 Danieau Buffer and harvested at 16 hpf", "tissue:embryonic cells|strain:AB|cell type:embryonic cells|genotype:angptl5 mutant|treatment:CRISPR/Cas9 knockout|batch:A5 16h", "GSM8960245", "GSM8960245: A5 /  16 hpf; Danio rerio; RNA Seq", "GSM8960245 r1", "GSM8960245", "1", "RNA from the barcoded cells was reverse transcribed  reagents from a Chromium Single Cell reagent kit 10X Genomics Libraries were prepared using Single Cell 3\u2032Library & gel Bead kit v3 10x Genomics  Cat# PN 1000268 according to the manufacturer's protocol for 7350 cell recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582260", null, null, "A5_16h-zebra_S1_L001_R1_001.fastq.gz A5_16h-zebra_S1_L001_R2_001.fastq.gz", "fastq fastq", 126632686800.0, 422108956.0, "GSM8960245 r1", "0:150 1:150", "A:31741347954;C:28608734203;G:22541136036;T:43733881512;N:7587095", 150, 150, null, null, 31741347954, 28608734203, 22541136036, 43733881512, 7587095, "SRX28623695", "SRS24895016", "SRA2121245", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-04-29", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [72588, "SRR22797023", "SRX18756814", "SRS16192272", "SRP413556", "PRJNA913420", "Nodal coordinates the anterior posterior patterning of germ layers and induces head formation in zebrafish explants.", "GSE221220", "Other", "Purpose: To investingate cell types in wild type zebrafish explants. Methods:  Wild type explants injected with phenol red were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 9 968 single cell transcriptomes were collected post stringent quality control measures. Conclusions: 6 Cell types  were identified  wild type explants mainly contains the anterior neural ectoderm and epidermis at 10 hpf. Overall design: Wild type zebrafish explants were harvested at 10hpf for scRNA seq.", null, "pubmed:37729057", null, "zebrafish wild type explant 10hpf", "GSM6856370", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:10hpf|genotype:wild type", "zebrafish wild type explant 10hpf", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar compressed  files included filtered gene bc matrices post running CellRanger pipeline", "zebrafish cells", "phenol red was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage  then  were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 10hpfcorresponding to embryonic developmental stage separately.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer\u2019s protocol for 10000 cells recovery.", "explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:10hpf|genotype:wild type", "GSM6856370", "GSM6856370: zebrafish wild type explant 10hpf; Danio rerio; RNA Seq", "GSM6856370 r1", "GSM6856370", "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413556", null, "loader:fastq load.py", "WT_10hpf_S1_L001_R1_001.fastq.gz WT_10hpf_S1_L001_R2_001.fastq.gz", "fastq fastq", 144284560800.0, 480948536.0, "GSM6856370 r1", "0:150 1:150", "A:61459567540;C:25433070866;G:24459703281;T:32928214337;N:4004776", 150, 150, null, null, 61459567540, 25433070866, 24459703281, 32928214337, 4004776, "SRX18756814", "SRS16192272", "SRA1561216", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.0, 0.92423, 0.0, 0.16334, 1.0, 0.78228, null, 0.51889, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-12-17", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [72740, "SRR23110572", "SRX19061958", "SRS16477633", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  DAPI neg", "GSM6940305", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940305", "GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq", "GSM6940305 r1", "GSM6940305", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_DAPI_neg-1_S17_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-1_S17_L001_R2_001.fastq.gz", "fastq fastq", 12188552084.0, 82667752.0, "GSM6940305 r1", "0:27 1:120.44", "A:3475006284;C:2574166578;G:2653428285;T:3480007630;N:5943307", 27, 120, null, null, 3475006284, 2574166578, 2653428285, 3480007630, 5943307, "SRX19061958", "SRS16477633", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00168, 0.91388, 0.00076, 0.19968, 0.99697, 0.85754, 0.48044, 0.49798, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72741, "SRR23110573", "SRX19061958", "SRS16477633", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  DAPI neg", "GSM6940305", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940305", "GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq", "GSM6940305 r1", "GSM6940305", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_DAPI_neg-2_S18_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-2_S18_L001_R2_001.fastq.gz", "fastq fastq", 13976267234.0, 94800658.0, "GSM6940305 r2", "0:27 1:120.43", "A:3999552660;C:2970812323;G:3076032177;T:3923173900;N:6696174", 27, 120, null, null, 3999552660, 2970812323, 3076032177, 3923173900, 6696174, "SRX19061958", "SRS16477633", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00195, 0.91588, 0.00083, 0.19869, 0.99659, 0.85788, 0.46543, 0.49295, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72742, "SRR23110574", "SRX19061958", "SRS16477633", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  DAPI neg", "GSM6940305", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940305", "GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq", "GSM6940305 r1", "GSM6940305", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_DAPI_neg-3_S19_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-3_S19_L001_R2_001.fastq.gz", "fastq fastq", 10663177356.0, 72321436.0, "GSM6940305 r3", "0:27 1:120.44", "A:3038724608;C:2260787836;G:2334365122;T:3024224853;N:5074937", 27, 120, null, null, 3038724608, 2260787836, 2334365122, 3024224853, 5074937, "SRX19061958", "SRS16477633", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00183, 0.91595, 0.00078, 0.19615, 0.99667, 0.85476, 0.42574, 0.51753, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72743, "SRR23110575", "SRX19061958", "SRS16477633", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  DAPI neg", "GSM6940305", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940305", "GSM6940305: 22 25 mm Adult Calvaria  DAPI neg; Danio rerio; RNA Seq", "GSM6940305 r1", "GSM6940305", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_DAPI_neg-4_S20_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_DAPI_neg-4_S20_L001_R2_001.fastq.gz", "fastq fastq", 11848567942.0, 80365988.0, "GSM6940305 r4", "0:27 1:120.43", "A:3428903160;C:2496116909;G:2566987382;T:3350843744;N:5716747", 27, 120, null, null, 3428903160, 2496116909, 2566987382, 3350843744, 5716747, "SRX19061958", "SRS16477633", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00179, 0.91204, 0.00085, 0.20828, 0.99715, 0.8717, 0.43575, 0.50701, 27, 118, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72744, "SRR23110576", "SRX19061957", "SRS16477632", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940304", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940304", "GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940304 r1", "GSM6940304", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz", "fastq fastq", 8988220186.0, 60952087.0, "GSM6940304 r1", "0:27 1:120.46", "A:2662713057;C:1786705322;G:2011325980;T:2520873526;N:6602301", 27, 120, null, null, 2662713057, 1786705322, 2011325980, 2520873526, 6602301, "SRX19061957", "SRS16477632", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00497, 0.89429, 0.00168, 0.18434, 0.99125, 0.8325, 0.54009, 0.54971, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72745, "SRR23110577", "SRX19061957", "SRS16477632", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940304", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940304", "GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940304 r1", "GSM6940304", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz", "fastq fastq", 10409092984.0, 70587244.0, "GSM6940304 r2", "0:27 1:120.46", "A:3082040103;C:2069527173;G:2331562542;T:2918295355;N:7667811", 27, 120, null, null, 3082040103, 2069527173, 2331562542, 2918295355, 7667811, "SRX19061957", "SRS16477632", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00486, 0.89223, 0.0016, 0.18706, 0.99095, 0.83382, 0.52631, 0.56473, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72746, "SRR23110578", "SRX19061957", "SRS16477632", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940304", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940304", "GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940304 r1", "GSM6940304", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz", "fastq fastq", 7852584028.0, 53251179.0, "GSM6940304 r3", "0:27 1:120.46", "A:2332795259;C:1555674536;G:1745851459;T:2212480038;N:5782736", 27, 120, null, null, 2332795259, 1555674536, 1745851459, 2212480038, 5782736, "SRX19061957", "SRS16477632", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00478, 0.89367, 0.0014, 0.1895, 0.99062, 0.83086, 0.53588, 0.55948, 27, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72747, "SRR23110579", "SRX19061957", "SRS16477632", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940304", null, "source name:calvaria|cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen|geo loc name:missing|collection date:missing", "22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:adult 22 25 mm|strain:tubingen", "GSM6940304", "GSM6940304: 22 25 mm Adult Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940304 r1", "GSM6940304", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 22-25_mm_Adult_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz", "fastq fastq", 11611263604.0, 78739888.0, "GSM6940304 r4", "0:27 1:120.46", "A:3440640044;C:2312536251;G:2595707458;T:3253782284;N:8597567", 27, 120, null, null, 3440640044, 2312536251, 2595707458, 3253782284, 8597567, "SRX19061957", "SRS16477632", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00481, 0.89424, 0.0015, 0.18882, 0.99115, 0.8325, 0.51954, 0.5663, 27, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Adult", "Adult", "Embryo Imprecise", "All anatomical structures"], [72748, "SRR23110580", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-1_S21_L001_R2_001.fastq.gz", "fastq fastq", 26193525700.0, 177672099.0, "GSM6940303 r1", "0:27 1:120.43", "A:7719827835;C:5410495858;G:5661676554;T:7386218620;N:15306833", 27, 120, null, null, 7719827835, 5410495858, 5661676554, 7386218620, 15306833, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88598, 0.00112, 0.18215, 0.99168, 0.77757, 0.47975, 0.51393, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72749, "SRR23110581", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-2_S22_L001_R2_001.fastq.gz", "fastq fastq", 20405308570.0, 138407397.0, "GSM6940303 r2", "0:27 1:120.43", "A:6066761212;C:4188427284;G:4382899879;T:5755324838;N:11895357", 27, 120, null, null, 6066761212, 4188427284, 4382899879, 5755324838, 11895357, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00368, 0.88942, 0.00119, 0.18885, 0.99184, 0.78693, 0.44927, 0.51797, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72750, "SRR23110582", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-3_S23_L001_R2_001.fastq.gz", "fastq fastq", 12307572438.0, 83482484.0, "GSM6940303 r3", "0:27 1:120.43", "A:3633520237;C:2534467756;G:2656045405;T:3476373726;N:7165314", 27, 120, null, null, 3633520237, 2534467756, 2656045405, 3476373726, 7165314, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.0038, 0.8858, 0.00113, 0.18267, 0.99101, 0.77699, 0.46833, 0.52027, 27, 121, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72751, "SRR23110583", "SRX19061956", "SRS16477631", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "GSM6940303", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940303", "GSM6940303: 9 11 mm Juvenile Calvaria  sp7GFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940303 r1", "GSM6940303", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_sp7GFPdepleted_DAPI_neg-4_S24_L001_R2_001.fastq.gz", "fastq fastq", 18938094183.0, 128455057.0, "GSM6940303 r4", "0:27 1:120.43", "A:5600343426;C:3891577388;G:4069279675;T:5365803260;N:11090434", 27, 120, null, null, 5600343426, 3891577388, 4069279675, 5365803260, 11090434, "SRX19061956", "SRS16477631", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00359, 0.88634, 0.00128, 0.18783, 0.99212, 0.77893, 0.48997, 0.50684, 27, 120, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72752, "SRR23110584", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-1_S1_L001_R2_001.fastq.gz", "fastq fastq", 11012858533.0, 74696398.0, "GSM6940302 r1", "0:27 1:120.43", "A:3253931864;C:2230032555;G:2516883171;T:3003935990;N:8074953", 27, 120, null, null, 3253931864, 2230032555, 2516883171, 3003935990, 8074953, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00603, 0.89151, 0.00212, 0.18091, 0.98849, 0.79634, 0.5277, 0.52269, 27, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72753, "SRR23110585", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-2_S2_L001_R2_001.fastq.gz", "fastq fastq", 10212715196.0, 69269302.0, "GSM6940302 r2", "0:27 1:120.43", "A:3014265330;C:2070878830;G:2341755898;T:2778343711;N:7471427", 27, 120, null, null, 3014265330, 2070878830, 2341755898, 2778343711, 7471427, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00554, 0.89174, 0.00191, 0.1793, 0.98884, 0.79732, 0.51857, 0.52305, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72754, "SRR23110586", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-3_S3_L001_R2_001.fastq.gz", "fastq fastq", 7996112551.0, 54234020.0, "GSM6940302 r3", "0:27 1:120.44", "A:2359724282;C:1611743954;G:1830950721;T:2187871443;N:5822151", 27, 120, null, null, 2359724282, 1611743954, 1830950721, 2187871443, 5822151, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00614, 0.88908, 0.00216, 0.1836, 0.98821, 0.79547, 0.52232, 0.51954, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72755, "SRR23110587", "SRX19061955", "SRS16477630", "SRP418118", "PRJNA925134", "BMP dependent cellular dynamics during cranial suture establishment in zebrafish", "GSE223147", "Transcriptome Analysis", "Cranial sutures separate neighboring skull bones and contain skeletal stem cells that drive bone growth. A key question is how osteogenic activity is controlled to promote bone growth while preventing aberrant bone fusions during skull expansion. Here we integrate single cell transcriptomics  in vivo expression validation  photoconversion based lineage tracing  and a zebrafish craniosynostosis model to uncover key developmental transitions regulating bone formation during skull expansion. In addition to conservation of meninges and osteoblast lineage cells between zebrafish and mouse  single cell transcriptomic analysis of the zebrafish skull reveals distinct subpopulations of suture mesenchyme that undergo transcriptomic changes during suture establishment. While lineage tracing with an osteoblast specific nlsEOS reporter shows that bone formation largely occurs at suture edges  a subset of mesenchyme cells in the mid suture region upregulate a suite of genes including BMP antagonists e.g. grem1a and pro angiogenic factors. Further  lineage tracing with grem1a:nlsEOS reveals that this mid suture subpopulation is largely non osteogenic. In twist1b; tcf12 mutant zebrafish  a model for the coronal synostosis of Saethre Chotzen Syndrome  reduction of grem1a+ mid suture cells correlates with misregulated bone formation and reduced blood vessels at the coronal suture. In addition  combinatorial mutation of BMP antagonists enriched in the mid suture subpopulation results in increased BMP signaling in the suture  misregulated bone formation  and abnormal suture morphology. These data support roles of a subset of mid suture mesenchyme in locally promoting BMP antagonism that ensures proper suture morphology. Overall design: Dissected calvaria of zebrafish were dissociated from juvenvile and adult zebrafish and live cells were identified by sorting for the absence of fluoresence sp7:GFP or ecad:YFP and the absence of DAPI using Fluorescence activated cell sorting FACS. Sorted cells were processed using 10X Genomics", null, "pubmed:39138165", null, "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "GSM6940302", null, "source name:calvaria|cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen|geo loc name:missing|collection date:missing", "9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg", "Data analysis was performed with Seurat version 4.1.1  and datasets were filtered by nFeature RNA > 200  nFeature RNA < 2500  and percent.mt < 25. Filtered cells were normalized with SCTransform and datasets were integrated based on the tutorial \u201cIntegration and Label Transfer\u201d from Seurat https://satijalab.org/seurat/archive/v3.0/integration.html. The data were processed using the FindNeighbors and FindClusters functions and data were visualized with UMAP 30 principal components. The osteogenic subset of the integrated Seurat object was converted into a Monocle cell dataset and Monocle was performed following the Monocle3 recommended parameters https://cole trapnell lab.github.io/monocle3/docs/trajectories/#learn graph. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files and rds files", "calvaria", null, "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer\u2019s solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz\u2019s L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer\u2019s instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", "The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments Protocol 20771. Zebrafish embryos Danio rerio were raised in embryo media at 28.5\u00b0C. For adults  in the institute vivarium according to Protocol 20771.", "cell type:various|tissue:calvaria|age:juvenile 9 11 mm|strain:tubingen", "GSM6940302", "GSM6940302: 9 11 mm Juvenile Calvaria  ecadYFPdepleted  DAPI neg; Danio rerio; RNA Seq", "GSM6940302 r1", "GSM6940302", "1", "We dissected the calvaria from 20 juvenile 9 11mm from ecad:YFP one dataset or sp7:GFP one dataset  and separately 10 adult 22 25 mm ecad:YFP one dataset or Tubingen one dataset  fish away from brain tissue in Ringer's solution. 9 11 mm stages Calvaria were mechanically minced with a razor and all tissue was transferred to a 1.5 mL tube for enzymatic dissociation 0.25% trypsin Life Technologies  15090 046  1\u2009mM EDTA  and 400\u2009mg/mL Collagenase D Sigma  11088882001 in PBS. Tissue was incubated on a nutator at 28.5\u2009\u00b0C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6\u2009mM CaCl2 and 30% fetal bovine serum FBS in PBS.  Cells were pelleted by centrifugation 300 g at 4\u2009\u00b0C  rinsed in suspension media 1% FBS  0.8\u2009mM CaCl2 Sigma Aldrich  St. Louis  MO in phenol red free Leibovitz's L15 medium Life Technologies  and resuspended in a final volume of 500 uL. DAPI was added to the resuspended cells  and cells were fluorescence activated cell sorted FACS to isolate live cells that were DAPI negative and when applicative  ecad:YFP/sp7:GFP negative to deplete epithelial cells. scRNAseq libraries were prepared using 10X Genomics Chromium Single Cell 3\u2032 Library and Gel Bead Kit v.2 according to the manufacturer's instructions and sequenced using Illumina NextSeq or HiSeq machines at a depth of at least 50 000 reads per cell for each library. Juvenile and adult stages were performed in replicates  and sequenced data was aligned using Cellranger v3.0.0 from 10X Genomics against the GRCz11 genome. All parameters were set to their default values.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418118", null, null, "9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R1_001.fastq.gz 9-11_mm_Juvenile_Calvaria_ecadYFPdepleted_DAPI_neg-4_S4_L001_R2_001.fastq.gz", "fastq fastq", 11056657034.0, 74991022.0, "GSM6940302 r4", "0:27 1:120.44", "A:3246337136;C:2242556246;G:2556848463;T:3002783409;N:8131780", 27, 120, null, null, 3246337136, 2242556246, 2556848463, 3002783409, 8131780, "SRX19061955", "SRS16477630", "SRA1576283", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", "Farmer Lab, Molecular, Cell and Developmental Biology; Department of Orthopaedic Surgery, University of California, Los Angeles", 2, 0.00621, 0.8906, 0.00194, 0.17648, 0.98762, 0.80133, 0.48802, 0.52225, 27, 121, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2023-01-18", "Juvenile", "Juvenile", "Embryo Imprecise", "All anatomical structures"], [72834, "SRR23210473", "SRX19158410", "SRS16570831", "SRP418915", "PRJNA927004", "Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization", "GSE223636", "Other", "Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods:  Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics  zebrafish embryos at 6 hpf were harvested.  Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm  which drives a differential expression of those key regulators  such as gsc and ripply1 in these two cell lineages  and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.", null, null, null, "zebrafish Nodal explants constructed from ndr1 morphants", "GSM6969676", null, "source name:zebrafish cells|strain:AB|tissue:embryonic cells|age:6hpf", "zebrafish Nodal explants constructed from ndr1 morphants", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or  gzip compressed  files included filtered gene bc matrices and ATAC fragments  post running CellRanger or cellranger arc pipeline.", "zebrafish cells", "10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage  then  were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer\u2019s protocol for 10000 cells recovery.", "Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:AB|tissue:embryonic cells|age:6hpf", "GSM6969676", "GSM6969676: zebrafish Nodal explants constructed from ndr1 morphants; Danio rerio; RNA Seq", "GSM6969676 r1", "GSM6969676", "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP418915", null, null, "ndr1Mo_cyc_6hpf_S5_L002_R1_001.fastq.gz ndr1Mo_cyc_6hpf_S5_L002_R2_001.fastq.gz", "fastq fastq", 82246861872.0, 464671536.0, "GSM6969676 r1", "0:26 1:151", "A:23306781803;C:17200141798;G:18609129782;T:23129217367;N:1591122", 26, 151, null, null, 23306781803, 17200141798, 18609129782, 23129217367, 1591122, "SRX19158410", "SRS16570831", "SRA1581154", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.00753, 0.93187, 0.00244, 0.09764, 0.9867, 0.79813, 0.42974, 0.53736, 26, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-01-24", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [72835, "SRR23210474", "SRX19158409", "SRS16570830", "SRP418915", "PRJNA927004", "Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization", "GSE223636", "Other", "Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods:  Nodal injected explants injected with 10pg ndr2 mRNA constructed from lft1 mutants and ndr1 morphants were harvested at xxxhpf. Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 according to the manufacturer's protocol for 10000 cells recovery. For single cell multiomics  zebrafish embryos at 6 hpf were harvested.  Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery. Results: A total of 10 614 single cell transcriptomes and 4 335 multiomics were collected post stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm  which drives a differential expression of those key regulators  such as gsc and ripply1 in these two cell lineages  and further regulates mesendoderm cell fate separation. Overall design: zebrafish Nodal explants constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf for scRNA seq. Zebrafish embryos were harvested at 6hpf for single cell multiomics.", null, null, null, "zebrafish Nodal explants constructed from lft1 mutants", "GSM6969675", null, "source name:zebrafish cells|strain:lft1 mutant|tissue:embryonic cells|age:6hpf", "zebrafish Nodal explants constructed from lft1 mutants", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 6.1.2 and cellranger arc version 2.0.0 with default parameters. Assembly: GRCz11 Supplementary files format and content: tar archivr or  gzip compressed  files included filtered gene bc matrices and ATAC fragments  post running CellRanger or cellranger arc pipeline.", "zebrafish cells", "10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at xxx cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage  then  were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf corresponding to embryonic developmental stage.", "Libraries were prepared using Chromium Controller and Chromium Single Cell 3\u2019Library & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer\u2019s protocol for 10000 cells recovery.", "Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium", "strain:lft1 mutant|tissue:embryonic cells|age:6hpf", "GSM6969675", "GSM6969675: zebrafish Nodal explants constructed from lft1 mutants; Danio rerio; RNA Seq", "GSM6969675 r1", "GSM6969675", "1", "Libraries were prepared using Chromium Controller and Chromium Single Cell three primeLibrary & Gel Bead Kit v3 10x Genomics  PN 1000075 and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics  4 rxns PN 1000285 according to the manufacturer's protocol for 10000 cells recovery.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP418915", null, null, "lft1Mu_cyc_6hpf_S1_L001_R1_001.fastq.gz lft1Mu_cyc_6hpf_S1_L001_R2_001.fastq.gz", "fastq fastq", 89053334922.0, 503126186.0, "GSM6969675 r1", "0:26 1:151", "A:26667371583;C:17898813431;G:19518773309;T:24966420492;N:1956107", 26, 151, null, null, 26667371583, 17898813431, 19518773309, 24966420492, 1956107, "SRX19158409", "SRS16570830", "SRA1581154", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.01205, 0.89743, 0.00297, 0.09338, 0.98082, 0.80961, 0.48847, 0.58599, 26, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-01-24", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74105, "SRR23380800", "SRX19321399", "SRS16719697", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  50% epiboly  NT  replicate B  scRNAseq", "GSM7035744", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo  50% epiboly  NT  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT", "GSM7035744", "GSM7035744: zebrafish embryo  50% epiboly  NT  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035744 r1", "GSM7035744", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B09_S9_I1_001.fastq.gz B09_S9_R1_001.fastq.gz B09_S9_R2_001.fastq.gz", "fastq fastq fastq", 1731750720.0, 10308040.0, "GSM7035744 r1", "0:8 1:20 2:140", "A:483160966;C:257831212;G:374014730;T:328009839;N:108853", 8, 20, 140, null, 483160966, 257831212, 374014730, 328009839, 108853, "SRX19321399", "SRS16719697", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.76439, null, 0.04865, null, 0.85794, null, 0.69865, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74106, "SRR23380801", "SRX19321398", "SRS16719698", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  50% epiboly  IAA  replicate B  scRNAseq", "GSM7035743", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  50% epiboly  IAA  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA", "GSM7035743", "GSM7035743: zebrafish embryo  50% epiboly  IAA  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035743 r1", "GSM7035743", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B10_S10_I1_001.fastq.gz B10_S10_R1_001.fastq.gz B10_S10_R2_001.fastq.gz", "fastq fastq fastq", 1449614208.0, 8628656.0, "GSM7035743 r1", "0:8 1:20 2:140", "A:383054921;C:231791450;G:292787007;T:300288679;N:89783", 8, 20, 140, null, 383054921, 231791450, 292787007, 300288679, 89783, "SRX19321398", "SRS16719698", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.69705, null, 0.03055, null, 0.86009, null, 0.49815, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74107, "SRR23380802", "SRX19321397", "SRS16719696", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  50% epiboly  NT  replicate A  scRNAseq", "GSM7035742", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo  50% epiboly  NT  replicate A  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:NT", "GSM7035742", "GSM7035742: zebrafish embryo  50% epiboly  NT  replicate A  scRNAseq; Danio rerio; RNA Seq", "GSM7035742 r1", "GSM7035742", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B03_S3_I1_001.fastq.gz B03_S3_R1_001.fastq.gz B03_S3_R2_001.fastq.gz", "fastq fastq fastq", 3289212696.0, 19578647.0, "GSM7035742 r1", "0:8 1:20 2:140", "A:917014925;C:511489537;G:636621002;T:675689845;N:195271", 8, 20, 140, null, 917014925, 511489537, 636621002, 675689845, 195271, "SRX19321397", "SRS16719696", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.84983, null, 0.0403, null, 0.84948, null, 0.66672, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74108, "SRR23380803", "SRX19321396", "SRS16719695", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  50% epiboly  IAA  replicate A  scRNAseq", "GSM7035741", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  50% epiboly  IAA  replicate A  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:50% epiboly|strain:AB/TL|treatment:IAA", "GSM7035741", "GSM7035741: zebrafish embryo  50% epiboly  IAA  replicate A  scRNAseq; Danio rerio; RNA Seq", "GSM7035741 r1", "GSM7035741", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B04_S4_R1_001.fastq.gz B04_S4_R2_001.fastq.gz B04_S4_I1_001.fastq.gz", "fastq fastq fastq", 18799793040.0, 111903530.0, "GSM7035741 r1", "0:8 1:20 2:140", "A:5320607436;C:2779767285;G:3920270375;T:3644700536;N:1148568", 8, 20, 140, null, 5320607436, 2779767285, 3920270375, 3644700536, 1148568, "SRX19321396", "SRS16719695", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.64644, null, 0.0354, null, 0.85886, null, 0.48293, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74109, "SRR23380804", "SRX19321395", "SRS16719694", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  zfs:0000015  NT  replicate B  scRNAseq", "GSM7035740", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo  zfs:0000015  NT  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT", "GSM7035740", "GSM7035740: zebrafish embryo  zfs:0000015  NT  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035740 r1", "GSM7035740", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B07_S7_I1_001.fastq.gz B07_S7_R1_001.fastq.gz B07_S7_R2_001.fastq.gz", "fastq fastq fastq", 5107507608.0, 30401831.0, "GSM7035740 r1", "0:8 1:20 2:140", "A:1271612661;C:768251429;G:1315055363;T:901018360;N:318527", 8, 20, 140, null, 1271612661, 768251429, 1315055363, 901018360, 318527, "SRX19321395", "SRS16719694", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.6633, null, 0.0322, null, 0.86898, null, 0.73112, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74110, "SRR23380805", "SRX19321394", "SRS16719693", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq", "GSM7035739", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA", "GSM7035739", "GSM7035739: zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035739 r1", "GSM7035739", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B08_S8_R2_001.fastq.gz B08_S8_R1_001.fastq.gz B08_S8_I1_001.fastq.gz", "fastq fastq fastq", 6618266424.0, 39394443.0, "GSM7035739 r1", "0:8 1:20 2:140", "A:1772472371;C:1058335373;G:1382074511;T:1301941080;N:398685", 8, 20, 140, null, 1772472371, 1058335373, 1382074511, 1301941080, 398685, "SRX19321394", "SRS16719693", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.66052, null, 0.03428, null, 0.84902, null, 0.4999, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74111, "SRR23380806", "SRX19321393", "SRS16719692", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  zfs:0000015  NT  replicate A  scRNAseq", "GSM7035738", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo  zfs:0000015  NT  replicate A  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:NT", "GSM7035738", "GSM7035738: zebrafish embryo  zfs:0000015  NT  replicate A  scRNAseq; Danio rerio; RNA Seq", "GSM7035738 r1", "GSM7035738", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B01_S1_I1_001.fastq.gz B01_S1_R1_001.fastq.gz B01_S1_R2_001.fastq.gz", "fastq fastq fastq", 2465114064.0, 14673298.0, "GSM7035738 r1", "0:8 1:20 2:140", "A:682033408;C:384987859;G:496372763;T:490717526;N:150164", 8, 20, 140, null, 682033408, 384987859, 496372763, 490717526, 150164, "SRX19321393", "SRS16719692", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.83566, null, 0.03718, null, 0.85021, null, 0.68773, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74112, "SRR23380807", "SRX19321392", "SRS16719691", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  zfs:0000015  IAA  replicate A  scRNAseq", "GSM7035737", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  zfs:0000015  IAA  replicate A  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA", "GSM7035737", "GSM7035737: zebrafish embryo  zfs:0000015  IAA  replicate A  scRNAseq; Danio rerio; RNA Seq", "GSM7035737 r1", "GSM7035737", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B02_S2_I1_001.fastq.gz B02_S2_R1_001.fastq.gz B02_S2_R2_001.fastq.gz", "fastq fastq fastq", 12337001376.0, 73434532.0, "GSM7035737 r1", "0:8 1:20 2:140", "A:3313181087;C:1943751072;G:2424458605;T:2598692748;N:750968", 8, 20, 140, null, 3313181087, 1943751072, 2424458605, 2598692748, 750968, "SRX19321392", "SRS16719691", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.73328, null, 0.03858, null, 0.84045, null, 0.49156, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74113, "SRR23380808", "SRX19321391", "SRS16719689", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  Dome  NT  replicate B  scRNAseq", "GSM7035736", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:NT|geo loc name:missing|collection date:missing", "zebrafish embryo  Dome  NT  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:NT", "GSM7035736", "GSM7035736: zebrafish embryo  Dome  NT  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035736 r1", "GSM7035736", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B05_S5_I1_001.fastq.gz B05_S5_R1_001.fastq.gz B05_S5_R2_001.fastq.gz", "fastq fastq fastq", 8803995984.0, 52404738.0, "GSM7035736 r1", "0:8 1:20 2:140", "A:2610393348;C:1221729748;G:1971221134;T:1532772530;N:546560", 8, 20, 140, null, 2610393348, 1221729748, 1971221134, 1532772530, 546560, "SRX19321391", "SRS16719689", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.6884, null, 0.03585, null, 0.86423, null, 0.72819, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74114, "SRR23380809", "SRX19321390", "SRS16719690", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  Dome  IAA  replicate B  scRNAseq", "GSM7035735", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  Dome  IAA  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:Dome|strain:AB/TL|treatment:IAA", "GSM7035735", "GSM7035735: zebrafish embryo  Dome  IAA  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035735 r1", "GSM7035735", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B06_S6_I1_001.fastq.gz B06_S6_R1_001.fastq.gz B06_S6_R2_001.fastq.gz", "fastq fastq fastq", 21140863800.0, 125838475.0, "GSM7035735 r1", "0:8 1:20 2:140", "A:6033328114;C:2907546987;G:4997520100;T:3677695966;N:1295333", 8, 20, 140, null, 6033328114, 2907546987, 4997520100, 3677695966, 1295333, "SRX19321390", "SRS16719690", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.54964, null, 0.01991, null, 0.86539, null, 0.48683, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74313, "SRR23635448", "SRX19518497", "SRS16905859", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  scRNAseq", "GSM7067528", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067528", "GSM7067528: KO  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067528 r1", "GSM7067528", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO2_S1_L001_R1_001.fastq.gz KO2_S1_L001_R2_001.fastq.gz", "fastq fastq", 53488401000.0, 178294670.0, "GSM7067528 r1", "0:150 1:150", "A:15827864442;C:8025310616;G:9015899201;T:20619013280;N:313461", 150, 150, null, null, 15827864442, 8025310616, 9015899201, 20619013280, 313461, "SRX19518497", "SRS16905859", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.34058, 0.91108, 0.13102, 0.21778, 0.9708, 0.77035, 0.53245, 0.49647, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74314, "SRR23635449", "SRX19518497", "SRS16905859", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  scRNAseq", "GSM7067528", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067528", "GSM7067528: KO  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067528 r1", "GSM7067528", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO2_S1_L002_R1_001.fastq.gz KO2_S1_L002_R2_001.fastq.gz", "fastq fastq", 60847932300.0, 202826441.0, "GSM7067528 r2", "0:150 1:150", "A:17985488985;C:9133506297;G:10281020307;T:23447556950;N:359761", 150, 150, null, null, 17985488985, 9133506297, 10281020307, 23447556950, 359761, "SRX19518497", "SRS16905859", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.35283, 0.91056, 0.13679, 0.21658, 0.97104, 0.76824, 0.51893, 0.50136, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74315, "SRR23635450", "SRX19518497", "SRS16905859", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  scRNAseq", "GSM7067528", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067528", "GSM7067528: KO  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067528 r1", "GSM7067528", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO2_S1_L003_R1_001.fastq.gz KO2_S1_L003_R2_001.fastq.gz", "fastq fastq", 67048274700.0, 223494249.0, "GSM7067528 r3", "0:150 1:150", "A:19858503269;C:10033315422;G:11285938910;T:25870120381;N:396718", 150, 150, null, null, 19858503269, 10033315422, 11285938910, 25870120381, 396718, "SRX19518497", "SRS16905859", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.34421, 0.91081, 0.12954, 0.21643, 0.96956, 0.7696, 0.53118, 0.50928, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74316, "SRR23635451", "SRX19518497", "SRS16905859", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 2  scRNAseq", "GSM7067528", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067528", "GSM7067528: KO  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067528 r1", "GSM7067528", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO2_S1_L004_R1_001.fastq.gz KO2_S1_L004_R2_001.fastq.gz", "fastq fastq", 10496177400.0, 34987258.0, "GSM7067528 r4", "0:150 1:150", "A:3095359531;C:1575341359;G:1780830304;T:4044583514;N:62692", 150, 150, null, null, 3095359531, 1575341359, 1780830304, 4044583514, 62692, "SRX19518497", "SRS16905859", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.33321, 0.91143, 0.12629, 0.21413, 0.97256, 0.76988, 0.51545, 0.50368, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74317, "SRR23635452", "SRX19518496", "SRS16905858", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  scRNAseq", "GSM7067527", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067527", "GSM7067527: KO  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067527 r1", "GSM7067527", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO1_S1_L001_R1_001.fastq.gz KO1_S1_L001_R2_001.fastq.gz", "fastq fastq", 46815268200.0, 156050894.0, "GSM7067527 r1", "0:150 1:150", "A:14262170825;C:6987175651;G:7568959746;T:17996793065;N:168913", 150, 150, null, null, 14262170825, 6987175651, 7568959746, 17996793065, 168913, "SRX19518496", "SRS16905858", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.29309, 0.91541, 0.11289, 0.20951, 0.97096, 0.77007, 0.51785, 0.50038, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74318, "SRR23635453", "SRX19518496", "SRS16905858", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  scRNAseq", "GSM7067527", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067527", "GSM7067527: KO  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067527 r1", "GSM7067527", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO1_S1_L002_R1_001.fastq.gz KO1_S1_L002_R2_001.fastq.gz", "fastq fastq", 57314766300.0, 191049221.0, "GSM7067527 r2", "0:150 1:150", "A:17411608554;C:8579243569;G:9305621852;T:22018087290;N:205035", 150, 150, null, null, 17411608554, 8579243569, 9305621852, 22018087290, 205035, "SRX19518496", "SRS16905858", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.29933, 0.91634, 0.11419, 0.21042, 0.97191, 0.77049, 0.49822, 0.50576, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74319, "SRR23635454", "SRX19518496", "SRS16905858", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  scRNAseq", "GSM7067527", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067527", "GSM7067527: KO  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067527 r1", "GSM7067527", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO1_S1_L003_R1_001.fastq.gz KO1_S1_L003_R2_001.fastq.gz", "fastq fastq", 49793178900.0, 165977263.0, "GSM7067527 r3", "0:150 1:150", "A:15157773060;C:7439911776;G:8061299298;T:19134016399;N:178367", 150, 150, null, null, 15157773060, 7439911776, 8061299298, 19134016399, 178367, "SRX19518496", "SRS16905858", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.29177, 0.91563, 0.11066, 0.20906, 0.97155, 0.77068, 0.52121, 0.5115, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74320, "SRR23635455", "SRX19518496", "SRS16905858", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "KO  replicate 1  scRNAseq", "GSM7067527", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out|geo loc name:missing|collection date:missing", "KO  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:tet2/3 double knock out", "GSM7067527", "GSM7067527: KO  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067527 r1", "GSM7067527", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "KO1_S1_L004_R1_001.fastq.gz KO1_S1_L004_R2_001.fastq.gz", "fastq fastq", 42201604800.0, 140672016.0, "GSM7067527 r4", "0:150 1:150", "A:12840927947;C:6302155191;G:6832707165;T:16225664045;N:150452", 150, 150, null, null, 12840927947, 6302155191, 6832707165, 16225664045, 150452, "SRX19518496", "SRS16905858", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.29701, 0.91511, 0.10937, 0.20946, 0.96976, 0.77088, 0.49807, 0.5099, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74321, "SRR23635456", "SRX19518495", "SRS16905856", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  scRNAseq", "GSM7067526", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067526", "GSM7067526: WT  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067526 r1", "GSM7067526", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT2_S1_L001_R1_001.fastq.gz WT2_S1_L001_R2_001.fastq.gz", "fastq fastq", 49142156100.0, 163807187.0, "GSM7067526 r1", "0:150 1:150", "A:14767624737;C:7242357270;G:8112643879;T:19018023780;N:1506434", 150, 150, null, null, 14767624737, 7242357270, 8112643879, 19018023780, 1506434, "SRX19518495", "SRS16905856", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.34617, 0.89671, 0.15927, 0.26698, 0.96558, 0.75921, 0.52649, 0.5163, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74322, "SRR23635457", "SRX19518495", "SRS16905856", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  scRNAseq", "GSM7067526", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067526", "GSM7067526: WT  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067526 r1", "GSM7067526", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT2_S1_L002_R1_001.fastq.gz WT2_S1_L002_R2_001.fastq.gz", "fastq fastq", 51781987200.0, 172606624.0, "GSM7067526 r2", "0:150 1:150", "A:15590160818;C:7611301035;G:8529863031;T:20049075878;N:1586438", 150, 150, null, null, 15590160818, 7611301035, 8529863031, 20049075878, 1586438, "SRX19518495", "SRS16905856", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.33909, 0.89639, 0.15069, 0.26703, 0.96396, 0.76086, 0.52555, 0.52062, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74323, "SRR23635458", "SRX19518495", "SRS16905856", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  scRNAseq", "GSM7067526", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067526", "GSM7067526: WT  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067526 r1", "GSM7067526", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT2_S1_L003_R1_001.fastq.gz WT2_S1_L003_R2_001.fastq.gz", "fastq fastq", 56660442600.0, 188868142.0, "GSM7067526 r3", "0:150 1:150", "A:17039975900;C:8339011401;G:9346860274;T:21932859284;N:1735741", 150, 150, null, null, 17039975900, 8339011401, 9346860274, 21932859284, 1735741, "SRX19518495", "SRS16905856", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.3429, 0.89693, 0.15175, 0.26945, 0.96418, 0.76116, 0.51192, 0.50989, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74324, "SRR23635459", "SRX19518495", "SRS16905856", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 2  scRNAseq", "GSM7067526", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 2  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067526", "GSM7067526: WT  replicate 2  scRNAseq; Danio rerio; RNA Seq", "GSM7067526 r1", "GSM7067526", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT2_S1_L004_R1_001.fastq.gz WT2_S1_L004_R2_001.fastq.gz", "fastq fastq", 37224225900.0, 124080753.0, "GSM7067526 r4", "0:150 1:150", "A:11192634168;C:5477522793;G:6137587586;T:14415351343;N:1130010", 150, 150, null, null, 11192634168, 5477522793, 6137587586, 14415351343, 1130010, "SRX19518495", "SRS16905856", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.33254, 0.89835, 0.15236, 0.26646, 0.96672, 0.76132, 0.51588, 0.51555, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74325, "SRR23635460", "SRX19518494", "SRS16905857", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  scRNAseq", "GSM7067525", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067525", "GSM7067525: WT  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067525 r1", "GSM7067525", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT1_S1_L001_R1_001.fastq.gz WT1_S1_L001_R2_001.fastq.gz", "fastq fastq", 65856223500.0, 219520745.0, "GSM7067525 r1", "0:150 1:150", "A:21355018202;C:9465269057;G:9803481122;T:25230563681;N:1891438", 150, 150, null, null, 21355018202, 9465269057, 9803481122, 25230563681, 1891438, "SRX19518494", "SRS16905857", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.32204, 0.8947, 0.14108, 0.2604, 0.96495, 0.75566, 0.5149, 0.51562, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74326, "SRR23635461", "SRX19518494", "SRS16905857", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  scRNAseq", "GSM7067525", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067525", "GSM7067525: WT  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067525 r1", "GSM7067525", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT1_S1_L002_R1_001.fastq.gz WT1_S1_L002_R2_001.fastq.gz", "fastq fastq", 61449324600.0, 204831082.0, "GSM7067525 r2", "0:150 1:150", "A:19856205943;C:8864345622;G:9209553919;T:23517461744;N:1757372", 150, 150, null, null, 19856205943, 8864345622, 9209553919, 23517461744, 1757372, "SRX19518494", "SRS16905857", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.32609, 0.89557, 0.14488, 0.25847, 0.96518, 0.75536, 0.50776, 0.51954, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74327, "SRR23635462", "SRX19518494", "SRS16905857", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  scRNAseq", "GSM7067525", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067525", "GSM7067525: WT  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067525 r1", "GSM7067525", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT1_S1_L003_R1_001.fastq.gz WT1_S1_L003_R2_001.fastq.gz", "fastq fastq", 64353459000.0, 214511530.0, "GSM7067525 r3", "0:150 1:150", "A:20842002225;C:9264260258;G:9604171241;T:24641180566;N:1844710", 150, 150, null, null, 20842002225, 9264260258, 9604171241, 24641180566, 1844710, "SRX19518494", "SRS16905857", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.32084, 0.89657, 0.13976, 0.25996, 0.96487, 0.75741, 0.51298, 0.51504, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74328, "SRR23635463", "SRX19518494", "SRS16905857", "SRP425043", "PRJNA939369", "The TET BMP regulatory axis in pathogenesis of CFM [scRNA]", "GSE226183", "Transcriptome Analysis", "Craniofacial microsomia CFM is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However  the molecular basis of CFM pathogenesis is largely unknown. Here we employ zebrafish model to investigate the mechanism of CFM pathogenesis. In early embryos  tet2 and tet3 are highly expressed and are essential for pharyngeal cartilage development. Single cell RNA sequencing and genetic analyses reveal that loss of Tet2/3 impaired chondrocyte differentiation largely due to insufficient BMP signaling. Mechanistically  Tet2/3 mediated 5 hydroxymethylcytosine modification allows the 5 hydroxymethylcytosine \u201creader\u201d  Sall4  to specifically bind the bmp4 promoter  thereby promoting bmp4 expression and enabling efficient BMP signaling. These findings indicate the TET BMP regulatory axis via 5 hydroxymethylcytosine to be critical for pharyngeal cartilage development. Whole exome sequencing of CFM patient samples show that single nucleotide polymorphisms in TET and BMP pathway genes increase the risk of CFM. Collectively  our study provides novel insights into understanding craniofacial development and CFM pathogenesis. Overall design: Single cell suspensions were processed for library construction using a Chromium Next GEM Single Cell 30 Reagent Kit v3 following the manufacturer's instructions. Libraries were then sequenced on the Illumina Novaseq 6000 platform.", "parent bioproject:PRJNA939357", "pubmed:38427557", null, "WT  replicate 1  scRNAseq", "GSM7067525", null, "source name:embryo|tissue:embryo|age:48 hpf|genotype:wild type|geo loc name:missing|collection date:missing", "WT  replicate 1  scRNAseq", "The demultiplexing  barcoded processing and gene counting were made using the Cell Ranger software v6.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: danrer11 Supplementary files format and content: Tab separated values files and matrix files", "embryo", null, "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer\u2019s instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "tissue:embryo|age:48 hpf|genotype:wild type", "GSM7067525", "GSM7067525: WT  replicate 1  scRNAseq; Danio rerio; RNA Seq", "GSM7067525 r1", "GSM7067525", "1", "The tissues of head regions from zebrafish embryos were washed in a phosphate buffered solution before adding dispase I Sigma  D4818 and incubated at 0.5U  33 \u00b0C for 10 min  with 750 rpm shock pipette every 30 s. post adding 100 \u03bcL of serum to stop digestion  tissues were filtered through a 70 \u03bcm mesh and a 20 \u03bcm mesh cell strainer  pelleted by centrifugation at 4 \u00b0C  and washed twice with ice cold HBSS adding 0.5 % BSA to remove debris. Single cell suspensions were processed for library construction following the manufacturer's instructions Chromium Next GEM Single Cell 30 Reagent Kits v3.1 User Guide. Libraries were then sequenced by Illumina Novaseq 6000 platform.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP425043", null, null, "WT1_S1_L004_R1_001.fastq.gz WT1_S1_L004_R2_001.fastq.gz", "fastq fastq", 54990712200.0, 183302374.0, "GSM7067525 r4", "0:150 1:150", "A:17796069746;C:7928926177;G:8221104962;T:21043035625;N:1575690", 150, 150, null, null, 17796069746, 7928926177, 8221104962, 21043035625, 1575690, "SRX19518494", "SRS16905857", "SRA1597330", "Yunnan University", "Yunnan University", 2, 0.31964, 0.89762, 0.14504, 0.26131, 0.96621, 0.75761, 0.50766, 0.51376, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-02-27", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [74458, "SRR23802705", "SRX19634573", "SRS17003744", "SRP426627", "PRJNA943249", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]", "GSE227117", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized  filtered  and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2", "GSM7091919", null, "source name:kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type|tissue:embryos|genotype:wild type", "kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type", "No treatments", "Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "tissue:embryos|genotype:wild type", "GSM7091919", "GSM7091919: kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2; Danio rerio; RNA Seq", "GSM7091919 r1", "GSM7091919", "1", "Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426627", null, null, "GR4_Single_Cell_TCTTACGC.fastq.sorted.fastq.gz", "fastq", 13661225700.0, 102550405.0, "GSM7091919 r1", "0:133.21", "A:4263167363;C:2771561232;G:2605236063;T:4020689114;N:571928", 133, null, null, null, 4263167363, 2771561232, 2605236063, 4020689114, 571928, "SRX19634573", "SRS17003744", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.64929, null, 0.08349, null, 0.80462, null, 0.50638, null, 149, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [74459, "SRR23802706", "SRX19634572", "SRS17003743", "SRP426627", "PRJNA943249", "Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche]", "GSE227117", "Transcriptome Analysis", "We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized  filtered  and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.", "parent bioproject:PRJNA510836", null, null, "kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1", "GSM7091918", null, "source name:kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type|tissue:embryos|genotype:wild type", "kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1", "the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode", "kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type", "No treatments", "Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", "Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.", "tissue:embryos|genotype:wild type", "GSM7091918", "GSM7091918: kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1; Danio rerio; RNA Seq", "GSM7091918 r1", "GSM7091918", "1", "Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP426627", null, null, "GR_Single_Cell_AGGCTTAG.fastq.sorted.fastq.gz", "fastq", 15177402828.0, 110023820.0, "GSM7091918 r1", "0:137.95", "A:4661865038;C:2940634835;G:2919070311;T:4655218796;N:613848", 137, null, null, null, 4661865038, 2940634835, 2919070311, 4655218796, 613848, "SRX19634572", "SRS17003743", null, null, "Oncology/Hematology, Boston Children's Hospital", 1, 0.73316, null, 0.12888, null, 0.79594, null, 0.5247, null, 127, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "indrops", null, "United States", "2023-03-10", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [74911, "SRR24149993", "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_S1_L001_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S1_L001_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 4058659523.0, 31957949.0, "GSM7165622 r1", "0:8 1:28 2:91", "A:896107265;C:594129789;G:680990539;T:736903719;N:42047", 8, 28, 91, null, 896107265, 594129789, 680990539, 736903719, 42047, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.86298, null, 0.17799, null, 0.7693, null, 0.52412, 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"], [74912, "SRR24149994", "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_S1_L002_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S1_L002_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 3866687339.0, 30446357.0, "GSM7165622 r2", "0:8 1:28 2:91", "A:851107575;C:567367968;G:649185168;T:702942598;N:15178", 8, 28, 91, null, 851107575, 567367968, 649185168, 702942598, 15178, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.86604, null, 0.17989, null, 0.77183, null, 0.52128, 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"], [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"], [74914, "SRR24149996", "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_L002_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S2_L002_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 3956093942.0, 31150346.0, "GSM7165622 r4", "0:8 1:28 2:91", "A:869028856;C:582249590;G:664516196;T:718871301;N:15543", 8, 28, 91, null, 869028856, 582249590, 664516196, 718871301, 15543, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.86787, null, 0.17834, null, 0.76995, null, 0.52486, 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"], [74915, "SRR24149997", "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_S3_L001_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L001_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 4078135608.0, 32111304.0, "GSM7165622 r5", "0:8 1:28 2:91", "A:899755177;C:596800898;G:684083008;T:741446772;N:42809", 8, 28, 91, null, 899755177, 596800898, 684083008, 741446772, 42809, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.8674, null, 0.18043, null, 0.76909, null, 0.52489, 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"], [74916, "SRR24149998", "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_S3_L002_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L002_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 3881456931.0, 30562653.0, "GSM7165622 r6", "0:8 1:28 2:91", "A:853798807;C:569305743;G:651609677;T:706472540;N:14656", 8, 28, 91, null, 853798807, 569305743, 651609677, 706472540, 14656, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.86918, null, 0.17885, null, 0.7671, null, 0.52606, 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"], [74917, "SRR24149999", "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_S4_L001_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S4_L001_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 3412026577.0, 26866351.0, "GSM7165622 r7", "0:8 1:28 2:91", "A:746679394;C:500559476;G:581227182;T:616336560;N:35329", 8, 28, 91, null, 746679394, 500559476, 581227182, 616336560, 35329, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.83361, null, 0.17225, null, 0.77289, null, 0.52617, 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"], [74918, "SRR24150000", "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_S4_L002_I1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S4_L002_R1_001.fastq.gz CEL200317AN_zebrafish_pLLP_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 3232756933.0, 25454779.0, "GSM7165622 r8", "0:8 1:28 2:91", "A:706026857;C:475261544;G:549948046;T:585135741;N:12701", 8, 28, 91, null, 706026857, 475261544, 549948046, 585135741, 12701, "SRX19948131", "SRS17296333", "SRA1622376", "Oregon Health and Science Univ", "Oregon Health and Science Univ", 1, 0.84189, null, 0.1719, null, 0.77392, null, 0.52102, 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"], [75394, "SRR24492134", "SRX20277377", "SRS17604630", "SRP436855", "PRJNA971152", "scRNAseq datasets supporting  a common precursor expression program leading to brain pericyte differentiation from neural crest and mesoderm", "GSE232163", "Transcriptome Analysis", "Brain pericytes are critical for regulating endothelial barrier function and activity  thus ensuring adequate blood flow to the brain. How the developmental acquisition of pericytes to naked endothelium is regulated  is largely unknown  but is relevant to disorders where vessels are poorly stabilized. Although pericytes are derived from neural crest and mesoderm  brain pericytes from both origins are currently indistinguishable; the genetic pathways leading to a convergent pericyte phenotype are unknown. We show here that a precursor population expressing the transcription factor nkx3.1 with origins in both NCC and mesoderm  develops into brain pericytes. We identify the gene signature of these precursors and show that an nkx3.1  foxf2a  and cxcl12b  expressing pericyte precursor population is present around the cxcr4 expressing basilar artery  and that these cells later spread throughout the brain. Cxcl12b  Cxcr4 signaling is required for pericyte attachment and differentiation but not for later pericyte development. Further  both nkx3.1 and cxcl12b are necessary and sufficient in regulating pericyte number. Thus  we have defined an undescribed population of pericyte precursors and identified genes critical for their differentiation. Overall design: Embryos expressing the nkx3.1NTR mcherry transgene were dissociated from wildtype 30 hpf zebrafish embryos and mCherry positive FACs sorted cells were subjected to single cell RNA sequencing. Two replicate libraries were generated from FACS sorted nkx3.1 expressing cells . To examine molecular changes within specific cell compartments  we isolated single cells from both biopsies and processed according to 10X Genomics Chromium Single Cell three prime Reagent Guidelines v3 Chemistry as per the manufacturer's protocol. In brief  single cells were sorted based on forward versus side scatter gating into 0.1% BSA\u2013PBS and partitioned into Gel Bead In EMulsions GEMs using 10x GemCodeTM Technology. Next Generation Sequencing was performed using the Illumina NovaSeq S2 Flow cells. All raw FASTQs were aligned to the human reference genome generated using cellranger mkref pipeline. The resulting gene barcode matrix was processed using Seurat R toolkit.", "parent bioproject:PRJNA973709", "pubmed:38683849", null, "Wildtype 30 hpf Zebrafish Embryo   Replicate 2", "GSM7316667", null, "source name:Embryo 2|tissue:embryo|age:30 hpf|transgenic strain:nkx3.1NTR mCherry|background:TL background|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor\u2122 780|library preparation:10X Genomics Single Cell RNAseq v3|geo loc name:missing|collection date:missing", "Wildtype 30 hpf Zebrafish Embryo   Replicate 2", "All raw FASTQs reads were aligned to Danio rerio zebrafish GRCz11 genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline  with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis. Assembly: Samples aligned to a custom Zebrafish Genome Assembly GRCz11 version 4.3.2 Lawson et al  eLife 2020 which is included in the GEO submission. Supplementary files format and content: Filtered gene   barcode matrix output from CellRanger", "Embryo 2", null, "Wildtype zebrafish embryos  expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene  were dissociated  assessed for viability  processed  resuspended in a designated solution  and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3\u2019 Reagent Guidelines v3 Chemistry. Briefly  single cells were sorted into 0.1% BSA\u2013HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA  generating full length cDNA from poly adenylated mRNA. DynaBeads\u00ae MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents  then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers  P7 primers  i7 sample index  and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.", null, "tissue:embryo|age:30 hpf|transgenic strain:nkx3.1NTR mCherry|background:TL background|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor\u2122 780|library preparation:10X Genomics Single Cell RNAseq v3", "GSM7316667", "GSM7316667: Wildtype 30 hpf Zebrafish Embryo   Replicate 2; Danio rerio; RNA Seq", "GSM7316667 r1", "GSM7316667", "1", "Wildtype zebrafish embryos  expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene  were dissociated  assessed for viability  processed  resuspended in a designated solution  and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell three prime Reagent Guidelines v3 Chemistry. Briefly  single cells were sorted into 0.1% BSA\u2013HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA  generating full length cDNA from poly adenylated mRNA. DynaBeads\u00ae MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents  then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers  P7 primers  i7 sample index  and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP436855", null, "dangling references:treat as unmapped|assembly:GRCz11|intentional duplicate", "S_2_count_possorted_genome_bam.bam", "10X Genomics bam file", 5745139764.0, 63133404.0, "GSM7316667 r1", "0:91", "A:1647050159;C:1282617598;G:1470594174;T:1344666383;N:211450", 91, null, null, null, 1647050159, 1282617598, 1470594174, 1344666383, 211450, "SRX20277377", "SRS17604630", "SRA1656031", "Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary", "Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary", 1, 0.90392, null, 0.1262, null, 0.81032, null, 0.46145, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2023-05-10", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75395, "SRR24492135", "SRX20277376", "SRS17604631", "SRP436855", "PRJNA971152", "scRNAseq datasets supporting  a common precursor expression program leading to brain pericyte differentiation from neural crest and mesoderm", "GSE232163", "Transcriptome Analysis", "Brain pericytes are critical for regulating endothelial barrier function and activity  thus ensuring adequate blood flow to the brain. How the developmental acquisition of pericytes to naked endothelium is regulated  is largely unknown  but is relevant to disorders where vessels are poorly stabilized. Although pericytes are derived from neural crest and mesoderm  brain pericytes from both origins are currently indistinguishable; the genetic pathways leading to a convergent pericyte phenotype are unknown. We show here that a precursor population expressing the transcription factor nkx3.1 with origins in both NCC and mesoderm  develops into brain pericytes. We identify the gene signature of these precursors and show that an nkx3.1  foxf2a  and cxcl12b  expressing pericyte precursor population is present around the cxcr4 expressing basilar artery  and that these cells later spread throughout the brain. Cxcl12b  Cxcr4 signaling is required for pericyte attachment and differentiation but not for later pericyte development. Further  both nkx3.1 and cxcl12b are necessary and sufficient in regulating pericyte number. Thus  we have defined an undescribed population of pericyte precursors and identified genes critical for their differentiation. Overall design: Embryos expressing the nkx3.1NTR mcherry transgene were dissociated from wildtype 30 hpf zebrafish embryos and mCherry positive FACs sorted cells were subjected to single cell RNA sequencing. Two replicate libraries were generated from FACS sorted nkx3.1 expressing cells . To examine molecular changes within specific cell compartments  we isolated single cells from both biopsies and processed according to 10X Genomics Chromium Single Cell three prime Reagent Guidelines v3 Chemistry as per the manufacturer's protocol. In brief  single cells were sorted based on forward versus side scatter gating into 0.1% BSA\u2013PBS and partitioned into Gel Bead In EMulsions GEMs using 10x GemCodeTM Technology. Next Generation Sequencing was performed using the Illumina NovaSeq S2 Flow cells. All raw FASTQs were aligned to the human reference genome generated using cellranger mkref pipeline. The resulting gene barcode matrix was processed using Seurat R toolkit.", "parent bioproject:PRJNA973709", "pubmed:38683849", null, "Wildtype 30 hpf Zebrafish Embryo   Replicate 1", "GSM7316666", null, "source name:Embryo 1|tissue:embryo|age:30 hpf|transgenic strain:nkx3.1NTR mCherry|background:TL background|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor\u2122 780|library preparation:10X Genomics Single Cell RNAseq v3|geo loc name:missing|collection date:missing", "Wildtype 30 hpf Zebrafish Embryo   Replicate 1", "All raw FASTQs reads were aligned to Danio rerio zebrafish GRCz11 genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline  with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis. Assembly: Samples aligned to a custom Zebrafish Genome Assembly GRCz11 version 4.3.2 Lawson et al  eLife 2020 which is included in the GEO submission. Supplementary files format and content: Filtered gene   barcode matrix output from CellRanger", "Embryo 1", null, "Wildtype zebrafish embryos  expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene  were dissociated  assessed for viability  processed  resuspended in a designated solution  and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3\u2019 Reagent Guidelines v3 Chemistry. Briefly  single cells were sorted into 0.1% BSA\u2013HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA  generating full length cDNA from poly adenylated mRNA. DynaBeads\u00ae MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents  then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers  P7 primers  i7 sample index  and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.", null, "tissue:embryo|age:30 hpf|transgenic strain:nkx3.1NTR mCherry|background:TL background|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor\u2122 780|library preparation:10X Genomics Single Cell RNAseq v3", "GSM7316666", "GSM7316666: Wildtype 30 hpf Zebrafish Embryo   Replicate 1; Danio rerio; RNA Seq", "GSM7316666 r1", "GSM7316666", "1", "Wildtype zebrafish embryos  expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene  were dissociated  assessed for viability  processed  resuspended in a designated solution  and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell three prime Reagent Guidelines v3 Chemistry. Briefly  single cells were sorted into 0.1% BSA\u2013HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA  generating full length cDNA from poly adenylated mRNA. DynaBeads\u00ae MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents  then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers  P7 primers  i7 sample index  and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP436855", null, "dangling references:treat as unmapped|assembly:GRCz11|intentional duplicate", "Suchit1_S1_count_possorted_genome_bam.bam", "10X Genomics bam file", 7670912158.0, 84295738.0, "GSM7316666 r1", "0:91", "A:2283938020;C:1611229026;G:1841446319;T:1934155829;N:142964", 91, null, null, null, 2283938020, 1611229026, 1841446319, 1934155829, 142964, "SRX20277376", "SRS17604631", "SRA1656031", "Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary", "Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary", 1, 0.88165, null, 0.21344, null, 0.79413, null, 0.57809, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2023-05-10", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 92, "expanded_columns": [], "expandable_columns": [], "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", 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