metadata: run_metadata: 92 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue

92 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
25127	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	mitfa high zf scRNAseq	GSM7706847	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		Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm 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 3’ 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.		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 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454647	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	5175410152	3650416721	4658958024	4315769305	24412	SRX21337840	SRS18583009	SRA1691286	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB	1	0.84133		0.13672		0.84756		0.52135		91		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25128	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	mitfa low zf scRNAseq	GSM7706846	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		Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm 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 3’ 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.		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 mg/ml pronase for 10 15 min deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454647	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	3674575574	2564940740	3313017210	3000585838	16688	SRX21337839	SRS18583008	SRA1691286	Pigment Cell Biology Lab, CSIR-IGIB	Pigment Cell Biology Lab, CSIR-IGIB	1	0.81163		0.13698		0.859		0.52032		91		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	unknown	sc	single_cell_droplet	10x	India	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25129	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 solu…			30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714	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	3982504087	2545259636	2793618614	3526744725	600557	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87401		0.26924		0.7517		0.5102		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25130	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 solu…			30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714	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	3499017196	2231848518	2450171440	3096822046	522278	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87457		0.27073		0.75278		0.50801		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25131	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 solu…			30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714	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	3147384451	2003642594	2200506573	2784120122	472442	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.873		0.27005		0.75122		0.5172		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
25132	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 solu…			30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos scRNAseq	GSM7708237	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP454714	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	3301539475	2111151786	2317995421	2926865071	493463	SRX21346683	SRS18591743	SRA1691311	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.87465		0.26977		0.75211		0.51651		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-11	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31872	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 48h	GSM8222580	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1824246454	1278127991	1448333280	1609791598	39243	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31873	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 48h	GSM8222580	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	2230570510	1564859730	1774018840	1969664072	48296	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31874	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 48h	GSM8222580	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	2205422432	1544223539	1750760277	1946533138	48071	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31875	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 48h	GSM8222580	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	326058980	228846142	262343444	285660694	7373	SRX24330059	SRS21091017	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Hatching	Embryo	Embryo Imprecise	All anatomical structures
31876	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 22h	GSM8222579	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1910521348	1357874019	1521970464	1690926373	41473	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31877	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 22h	GSM8222579	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	2016694527	1436202913	1608693558	1786117733	43726	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31878	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 22h	GSM8222579	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1443225941	1028068269	1151922277	1276632644	31673	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31879	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 22h	GSM8222579	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1873119195	1332238982	1493221194	1658936897	40665	SRX24330058	SRS21091016	SRA1850361	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-22	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31880	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 14h	GSM8216056	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1195361841	933687818	1057254177	1048237872	26812	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31881	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 14h	GSM8216056	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1320007258	1029906863	1166350676	1155370144	30148	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31882	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 14h	GSM8216056	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1273032152	992961980	1124384567	1115177910	28930	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31883	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 7…			CEL210312AN WT 14h	GSM8216056	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP502657	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	1412426673	1104618149	1250890162	1238194657	32156	SRX24303940	SRS21066774	SRA1848682	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-18	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
31972	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1233470398	840754101	925102747	1102656199	122563	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31973	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1245735118	849017838	935656364	1113856043	100681	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31974	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1411724640	961558289	1057832581	1261091330	139273	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31975	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1422617276	968975306	1067723068	1271232295	116175	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31976	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1121297258	765571677	841433529	1002663097	109787	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31977	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1131659183	772616863	850242289	1012253749	91380	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31978	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1221772454	832992882	915744544	1093089728	121144	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
31979	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 “pioneer” 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° 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° 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° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added an…			scRNAseq	GSM8244692	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP505049	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	1233691562	840924973	926085790	1103887111	99607	SRX24414680	SRS21169984	SRA1856329	Oregon Health and Science Univ	Oregon Health and Science Univ												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-04-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
33008	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.			Bmp4 explant 24h	GSM8366755	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		13643133254	11126085942	11676909916	12651522663	1132519	SRX25138332	SRS21830414	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33009	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.			Bmp4 explant 18h	GSM8366754	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		12441486571	10199111519	10790306255	11430847129	1329327	SRX25138331	SRS21830413	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33010	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.			Bmp4 explant 12h	GSM8366753	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		14089229753	10936347905	11403388741	13708020723	1141625	SRX25138330	SRS21830412	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33011	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.			Bmp4 explant 10h	GSM8366752	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		44020073879	31344780625	29505876494	44289819189	3997513	SRX25138329	SRS21830410	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33012	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.			Bmp4 explant 8h	GSM8366751	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		35474636770	23305712896	22894585568	37031410017	2773349	SRX25138328	SRS21830409	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33013	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.			Bmp4 explant 6h	GSM8366750	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 μl of an aggregation medium based on TeSR E6 and supplemented with the ROCK inhibitor 10μM 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 μl 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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer’s protocol for 10000 cell recovery.	Bmp4 explants were cultured in Dulbecco's modified Eagle’s medium DMEM/F 12 with 10 mM HEPES 1x MEM with non essential amino acids 7 mM CaCl2 1 mM sodium pyruvate 50 μg/ml gentamycin 100 μM 2 mercaptoethanol 1× antibiotic antimycotic 10% serum replacement and kept at 28.5℃.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′Library & gel Bead kit v3.1 10x Genomics Cat# PN 1000121 according to the manufacturer's protocol for 10000 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP516621		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		14755432217	11271293276	11858476334	14700289448	1154697	SRX25138327	SRS21830411	SRA1911917	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-06-27	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures
33617	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.		pubmed:39345358;pubmed:40171762	cranial NCCs YM	GSM8464445	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’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˚C 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 Next…		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˚C 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 Next…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP526857		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		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	United States	2024-08-16	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
33618	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.		pubmed:39345358;pubmed:40171762	cranial NCCs DMSO	GSM8464444	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’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˚C 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 Next…		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˚C 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 Next…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP526857		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		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		0.5212	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-16	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
35979	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× 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.			A5 / 16 hpf	GSM8960245	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′Library & gel Bead kit v3 10x Genomics Cat# PN 1000268 according to the manufacturer’s protocol for 7350 cell recovery.	The angptl5Δ10/Δ10 embryos were raised in 0.3× 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′Library & gel Bead kit v3 10x Genomics Cat# PN 1000268 according to the manufacturer's protocol for 7350 cell recovery.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP582260		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		31741347954	28608734203	22541136036	43733881512	7587095	SRX28623695	SRS24895016	SRA2121245	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University												T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-04-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
72588	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.		pubmed:37729057	zebrafish wild type explant 10hpf	GSM6856370	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’Library & Gel Bead Kit v3 10x Genomics PN 1000075 according to the manufacturer’s 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP413556	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		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		0.51889	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2022-12-17	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72740	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		pubmed:39138165	22 25 mm Adult Calvaria DAPI neg	GSM6940305	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72741	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		pubmed:39138165	22 25 mm Adult Calvaria DAPI neg	GSM6940305	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72742	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		pubmed:39138165	22 25 mm Adult Calvaria DAPI neg	GSM6940305	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72743	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		pubmed:39138165	22 25 mm Adult Calvaria DAPI neg	GSM6940305	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72744	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		pubmed:39138165	22 25 mm Adult Calvaria ecadYFPdepleted DAPI neg	GSM6940304	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72745	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		pubmed:39138165	22 25 mm Adult Calvaria ecadYFPdepleted DAPI neg	GSM6940304	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72746	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		pubmed:39138165	22 25 mm Adult Calvaria ecadYFPdepleted DAPI neg	GSM6940304	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72747	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		pubmed:39138165	22 25 mm Adult Calvaria ecadYFPdepleted DAPI neg	GSM6940304	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Adult	Adult	Embryo Imprecise	All anatomical structures
72748	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		pubmed:39138165	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72749	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		pubmed:39138165	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72750	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		pubmed:39138165	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72751	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		pubmed:39138165	9 11 mm Juvenile Calvaria sp7GFPdepleted DAPI neg	GSM6940303	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72752	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		pubmed:39138165	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72753	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		pubmed:39138165	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72754	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		pubmed:39138165	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72755	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		pubmed:39138165	9 11 mm Juvenile Calvaria ecadYFPdepleted DAPI neg	GSM6940302	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 “Integration and Label Transfer” 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		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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	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°C. 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 mM EDTA and 400 mg/mL Collagenase D Sigma 11088882001 in PBS. Tissue was incubated on a nutator at 28.5 °C for 45 min and the enzymatic reaction was stopped by adding 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Cells were pelleted by centrifugation 300 g at 4 °C rinsed in suspension media 1% FBS 0.8 mM 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′ 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP418118		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		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	United States	2023-01-18	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
72834	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.			zebrafish Nodal explants constructed from ndr1 morphants	GSM6969676	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’Library & 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.	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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP418915		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		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	China	2023-01-24	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
72835	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.			zebrafish Nodal explants constructed from lft1 mutants	GSM6969675	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’Library & 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.	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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP418915		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		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	China	2023-01-24	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
74105	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	zebrafish embryo 50% epiboly NT replicate B scRNAseq	GSM7035744	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	483160966	257831212	374014730	328009839	108853	SRX19321399	SRS16719697	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.76439		0.04865		0.85794		0.69865		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
74106	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	zebrafish embryo 50% epiboly IAA replicate B scRNAseq	GSM7035743	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	383054921	231791450	292787007	300288679	89783	SRX19321398	SRS16719698	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.69705		0.03055		0.86009		0.49815		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
74107	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	zebrafish embryo 50% epiboly NT replicate A scRNAseq	GSM7035742	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	917014925	511489537	636621002	675689845	195271	SRX19321397	SRS16719696	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.84983		0.0403		0.84948		0.66672		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
74108	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	zebrafish embryo 50% epiboly IAA replicate A scRNAseq	GSM7035741	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	5320607436	2779767285	3920270375	3644700536	1148568	SRX19321396	SRS16719695	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.64644		0.0354		0.85886		0.48293		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
74109	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	zebrafish embryo zfs:0000015 NT replicate B scRNAseq	GSM7035740	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	1271612661	768251429	1315055363	901018360	318527	SRX19321395	SRS16719694	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.6633		0.0322		0.86898		0.73112		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74110	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	zebrafish embryo zfs:0000015 IAA replicate B scRNAseq	GSM7035739	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	1772472371	1058335373	1382074511	1301941080	398685	SRX19321394	SRS16719693	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.66052		0.03428		0.84902		0.4999		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74111	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	zebrafish embryo zfs:0000015 NT replicate A scRNAseq	GSM7035738	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	682033408	384987859	496372763	490717526	150164	SRX19321393	SRS16719692	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.83566		0.03718		0.85021		0.68773		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74112	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	zebrafish embryo zfs:0000015 IAA replicate A scRNAseq	GSM7035737	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	3313181087	1943751072	2424458605	2598692748	750968	SRX19321392	SRS16719691	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.73328		0.03858		0.84045		0.49156		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74113	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	zebrafish embryo Dome NT replicate B scRNAseq	GSM7035736	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	2610393348	1221729748	1971221134	1532772530	546560	SRX19321391	SRS16719689	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.6884		0.03585		0.86423		0.72819		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74114	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	zebrafish embryo Dome IAA replicate B scRNAseq	GSM7035735	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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.		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°C 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 50–100 STAMPs were included in each 50uL PCR reaction and 12–13 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP422528	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	6033328114	2907546987	4997520100	3677695966	1295333	SRX19321390	SRS16719690	SRA1590430	Hebrew University of Jerusalem	Hebrew University of Jerusalem	1	0.54964		0.01991		0.86539		0.48683		140		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	dropseq	Israel	2023-02-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
74313	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 “reader” 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	KO replicate 2 scRNAseq	GSM7067528	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74314	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 “reader” 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	KO replicate 2 scRNAseq	GSM7067528	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74315	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 “reader” 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	KO replicate 2 scRNAseq	GSM7067528	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74316	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 “reader” 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	KO replicate 2 scRNAseq	GSM7067528	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74317	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 “reader” 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	KO replicate 1 scRNAseq	GSM7067527	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74318	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 “reader” 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	KO replicate 1 scRNAseq	GSM7067527	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74319	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 “reader” 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	KO replicate 1 scRNAseq	GSM7067527	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74320	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 “reader” 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	KO replicate 1 scRNAseq	GSM7067527	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74321	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 “reader” 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	WT replicate 2 scRNAseq	GSM7067526	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74322	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 “reader” 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	WT replicate 2 scRNAseq	GSM7067526	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74323	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 “reader” 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	WT replicate 2 scRNAseq	GSM7067526	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74324	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 “reader” 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	WT replicate 2 scRNAseq	GSM7067526	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74325	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 “reader” 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	WT replicate 1 scRNAseq	GSM7067525	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74326	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 “reader” 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	WT replicate 1 scRNAseq	GSM7067525	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74327	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 “reader” 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	WT replicate 1 scRNAseq	GSM7067525	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74328	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 “reader” 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	WT replicate 1 scRNAseq	GSM7067525	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		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.		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 °C for 10 min with 750 rpm shock pipette every 30 s. post adding 100 μL of serum to stop digestion tissues were filtered through a 70 μm mesh and a 20 μm mesh cell strainer pelleted by centrifugation at 4 °C 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP425043		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		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	China	2023-02-27	Hatching	Embryo	Embryo Imprecise	All anatomical structures
74458	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		kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep2	GSM7091919	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426627		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			4263167363	2771561232	2605236063	4020689114	571928	SRX19634573	SRS17003744			Oncology/Hematology, Boston Children's Hospital	1	0.64929		0.08349		0.80462		0.50638		149		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Embryo Imprecise	All anatomical structures
74459	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		kdrl:GFP+ mrc1a.125:GFP+ 72 hpf rep1	GSM7091918	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	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP426627		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			4661865038	2940634835	2919070311	4655218796	613848	SRX19634572	SRS17003743			Oncology/Hematology, Boston Children's Hospital	1	0.73316		0.12888		0.79594		0.5247		127		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	indrops	United States	2023-03-10	Larval	Larval	Embryo Imprecise	All anatomical structures
74911	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	896107265	594129789	680990539	736903719	42047	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86298		0.17799		0.7693		0.52412		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74912	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	851107575	567367968	649185168	702942598	15178	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86604		0.17989		0.77183		0.52128		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74913	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	915445002	610150205	697623249	754003095	43467	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86488		0.1772		0.77053		0.52905		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74914	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	869028856	582249590	664516196	718871301	15543	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86787		0.17834		0.76995		0.52486		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74915	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	899755177	596800898	684083008	741446772	42809	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.8674		0.18043		0.76909		0.52489		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74916	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	853798807	569305743	651609677	706472540	14656	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.86918		0.17885		0.7671		0.52606		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74917	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	746679394	500559476	581227182	616336560	35329	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.83361		0.17225		0.77289		0.52617		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
74918	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 mChe…		pubmed:37131612;pubmed:38165177	Tg 8.0claudinB: lynGFPzf106; TgBACcxcr4b:F tractin mCherry transgenic line scRNAseq	GSM7165622	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		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl PBS/ 2% BSA in a siliconized 1.5mL tube Library was performed according to the manufacturer’s instructions single cell 3’ v3 protocol 10x Genomics.		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° 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° 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° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm 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 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP432326	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	706026857	475261544	549948046	585135741	12701	SRX19948131	SRS17296333	SRA1622376	Oregon Health and Science Univ	Oregon Health and Science Univ	1	0.84189		0.1719		0.77392		0.52102		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-04-12	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
75394	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–PBS and partitioned into Gel Bead In EMulsions GEMs using 10x GemCodeTM Technology. Next Generation Sequencing was performed using the Illumina NovaSeq S2 Flow c…	parent bioproject:PRJNA973709	pubmed:38683849	Wildtype 30 hpf Zebrafish Embryo Replicate 2	GSM7316667	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™ 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		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’ Reagent Guidelines v3 Chemistry. Briefly single cells were sorted into 0.1% BSA–HBSS 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® 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.		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™ 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–HBSS 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® 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP436855	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			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		0.1262		0.81032		0.46145		91		B		usable mapping rate	illumina	novaseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2023-05-10	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
75395	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–PBS and partitioned into Gel Bead In EMulsions GEMs using 10x GemCodeTM Technology. Next Generation Sequencing was performed using the Illumina NovaSeq S2 Flow c…	parent bioproject:PRJNA973709	pubmed:38683849	Wildtype 30 hpf Zebrafish Embryo Replicate 1	GSM7316666	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™ 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		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’ Reagent Guidelines v3 Chemistry. Briefly single cells were sorted into 0.1% BSA–HBSS 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® 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.		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™ 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–HBSS 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® 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP436855	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			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		0.21344		0.79413		0.57809		91		B		usable mapping rate	illumina	novaseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	Canada	2023-05-10	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;