metadata: run_metadata: 313 rows where experiment.library_selection = "cDNA", technology = "10x" and tissue

313 rows where experiment.library_selection = "cDNA", technology = "10x" 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.description	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.attributes	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
30012	30012	SRR28164886	SRX23795142	SRS20618185	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 36 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 36 hpf CMO	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf CMO\|dev stage:36 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 36 hpf CMO	C 3	C 3	10x Genomics multiplexing CMO			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		36h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 36h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	42856660500.0	142855535.0	36h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:8992350191;C:10354632010;G:13923089582;T:9585439035;N:1149682	150	150		8992350191	10354632010	13923089582	9585439035	1149682	SRX23795142	SRS20618185	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30013	30013	SRR28164887	SRX23795141	SRS20618186	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 24 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 24 hpf CMO	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf CMO\|dev stage:24 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 24 hpf CMO	C 2	C 2	10x Genomics multiplexing CMO			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		24h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 24h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	45212181900.0	150707273.0	24h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:9741878752;C:11183590476;G:14447932886;T:9837582173;N:1197613	150	150		9741878752	11183590476	14447932886	9837582173	1197613	SRX23795141	SRS20618186	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30014	30014	SRR28164888	SRX23795140	SRS20618184	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing CMO	scRNA seq wild type and hamp / 12 hpf CMO	Zebrafish embryo scRNA seq wild type and hamp / 12 hpf CMO	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf CMO\|dev stage:12 hpf CMO\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 12 hpf CMO	C 1	C 1	10x Genomics multiplexing CMO			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz	fastq fastq	23801259900.0	79337533.0	12h Multiplexing Capture S1 L001 R1 001.fastq.gz	0:150 1:150	A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734	150	150		5110000752	5818733743	7758205963	5113684708	634734	SRX23795140	SRS20618184	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.0	0.0	0.0	0.0	1.0	1.0			150	150	T	T	mates < 9% mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
30015	30015	SRR28164889	SRX23795139	SRS20618183	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 36 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 36 hpf GEX	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:36 hpf GEX\|dev stage:36 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 36 hpf GEX	G 3	G 3	10x Genomics multiplexing GEX			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		36h_Gene_Expression_S1_L001_R2_001.fastq.gz 36h_Gene_Expression_S1_L001_R1_001.fastq.gz	fastq fastq	140285088600.0	467616962.0	36h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:41651884464;C:24916307056;G:25991077208;T:47722140024;N:3679848	150	150		41651884464	24916307056	25991077208	47722140024	3679848	SRX23795139	SRS20618183	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00148	0.91873	0.0	0.15509	0.99985	0.78086	0.57142	0.52919	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30016	30016	SRR28164890	SRX23795138	SRS20618182	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 24 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 24 hpf GEX	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:24 hpf GEX\|dev stage:24 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 24 hpf GEX	G 2	G 2	10x Genomics multiplexing GEX			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		24h_Gene_Expression_S1_L001_R1_001.fastq.gz 24h_Gene_Expression_S1_L001_R2_001.fastq.gz	fastq fastq	147407645100.0	491358817.0	24h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:43802123106;C:26617386219;G:27720887375;T:49263400239;N:3848161	150	150		43802123106	26617386219	27720887375	49263400239	3848161	SRX23795138	SRS20618182	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00129	0.92038	0.00042	0.15021	0.99993	0.77581	0.33333	0.51584	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
30017	30017	SRR28164891	SRX23795137	SRS20618181	SRP485064	PRJNA1067370	zebrafish embryo for scRNA seq and bulk RNA seq	PRJNA1067370	Other	Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.			10x Genomics multiplexing GEX	scRNA seq wild type and hamp / 12 hpf GEX	Zebrafish embryo scRNA seq wild type and hamp / 12 hpf GEX	strain:not applicable\|isolate:not collected\|breed:Danio\|cultivar:not applicable\|ecotype:not applicable\|age:12 hpf GEX\|dev stage:12 hpf GEX\|collection date:2022 10\|geo loc name:not applicable\|sex:not applicable\|tissue:embryo\|genotype:WT/hamp knockdown\|sample type:whole organism\|BioSampleModel:Model organism or animal									scRNA seq wild type and hamp / 12 hpf GEX	G 1	G 1	10x Genomics multiplexing GEX			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP485064		12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz	fastq fastq	204426398700.0	681421329.0	12h Gene Expression S1 L001 R1 001.fastq.gz	0:150 1:150	A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847	150	150		61302872939	35072603645	37153666376	70891933893	5321847	SRX23795137	SRS20618181	SRA1813495	Shanghai Ocean University\|College of Fisheries and Life	Shanghai Ocean University	2	0.00085	0.9058	0.0	0.12081	0.99991	0.80231	0.5	0.52456	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-02-29	Segmentation	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
32783	32783	SRR29438460	SRX24951082	SRS21654793	SRP514388	PRJNA1124950	Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution	GSE270075	Transcriptome Analysis	The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.		pubmed:39846194		Zebra PS	GSM8334032	source name:embryos\|tissue:embryos\|Stage:120 hpf\|treatment:PS20nm exposure\|geo loc name:missing\|collection date:missing	Zebra PS	First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx	embryos		The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		tissue:embryos\|Stage:120 hpf\|treatment:PS20nm exposure	GSM8334032	GSM8334032: Zebra PS; Danio rerio; RNA Seq	GSM8334032 r1	GSM8334032	1	The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP514388		Zebra_PS_S1_L003_R2_001.fastq.gz Zebra_PS_S1_L003_R1_001.fastq.gz	fastq fastq	46515993156.0	400999941.0	GSM8334032 r1	0:26 1:90	A:10540890310;C:12256097063;G:11432529211;T:12270960287;N:15516285	26	90		10540890310	12256097063	11432529211	12270960287	15516285	SRX24951082	SRS21654793	SRA1904713	Pusan National University	Pusan National University	2	0.07013	0.96133	0.0269	0.15067	0.98135	0.78849	0.31441	0.54509	26	90	T	B	sc-like readlen	illumina	hiseq_era	5prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	South Korea	2024-06-17	Larval	Larval	Embryo Imprecise	All anatomical structures
32784	32784	SRR29438461	SRX24951081	SRS21654792	SRP514388	PRJNA1124950	Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution	GSE270075	Transcriptome Analysis	The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied with a focus on oxidative stress and inflammatory responses. However this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally heme synthesis was impaired leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.		pubmed:39846194		Zebra Control	GSM8334031	source name:embryos\|tissue:embryos\|Stage:120 hpf\|treatment:Wild type\|geo loc name:missing\|collection date:missing	Zebra Control	First the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104 and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene per barcode. Also clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv features.tsv matrix.mtx	embryos		The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		tissue:embryos\|Stage:120 hpf\|treatment:Wild type	GSM8334031	GSM8334031: Zebra Control; Danio rerio; RNA Seq	GSM8334031 r1	GSM8334031	1	The samples were carefully resuspended in a cold calcium and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems catalog number F23001. Following this the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech catalog number 130 090 101 and MS columns Miltenyi Biotech catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics document number CG000331 Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics PN 1000244. In brief the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction where barcoded full length cDNA was synthesized from mRNA the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP514388		Zebra_Control_S1_L002_R1_001.fastq.gz Zebra_Control_S1_L002_R2_001.fastq.gz	fastq fastq	44451768632.0	383204902.0	GSM8334031 r1	0:26 1:90	A:10119968829;C:11732695259;G:10981098564;T:11603155786;N:14850194	26	90		10119968829	11732695259	10981098564	11603155786	14850194	SRX24951081	SRS21654792	SRA1904713	Pusan National University	Pusan National University	2	0.07283	0.96543	0.02838	0.15165	0.98052	0.78464	0.32149	0.56384	26	90	T	B	sc-like readlen	illumina	hiseq_era	5prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	South Korea	2024-06-17	Larval	Larval	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
48048	48048	SRR6956074	SRX3899097	SRS3136394	SRP137889	PRJNA449093	10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage	GSE112824	Transcriptome Analysis	Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch.	parent bioproject:PRJNA417291	pubmed:29700225		MZoep zebrafish embryo 6 somite	GSM3084403	tissue:Maternal Zygotic oep tz57 Mutant Embryo\|genotype/variation:MZoep mutant\|developmental stage:6 somite\|hpf	MZoep zebrafish embryo 6 somite	Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command "cellranger mkfastq" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command "cellranger count" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by "cellranger count" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by "cellranger count".	Maternal Zygotic oep tz57 Mutant Embryo		Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.	Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.	genotype/variation:MZoep mutant\|developmental stage:6 somite\|hpf	GSM3084403	GSM3084403: MZoep zebrafish embryo 6 somite; Danio rerio; RNA Seq	GSM3084403		1	Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.	GEO Accession:GSM3084403	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP137889	dangling references:treat as unmapped	10xMZoep6S_possorted_genome_bam.bam	10X Genomics bam file	6798121188.0	117208986.0	GSM3084403 r1	0:58	A:1967536512;C:1404909465;G:1675749247;T:1735311022;N:14614942	58			1967536512	1404909465	1675749247	1735311022	14614942	SRX3899097	SRS3136394	SRA683448	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.9431		0.07175		0.84439		0.49587		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-04-06	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
48049	48049	SRR6956073	SRX3899096	SRS3136393	SRP137889	PRJNA449093	10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage	GSE112824	Transcriptome Analysis	Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch.	parent bioproject:PRJNA417291	pubmed:29700225		WT zebrafish embryo 6 somite	GSM3084402	tissue:Wild type TLAB Embryo\|genotype/variation:wild type TLAB\|developmental stage:6 somite\|hpf	WT zebrafish embryo 6 somite	Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command "cellranger mkfastq" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command "cellranger count" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by "cellranger count" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by "cellranger count".	Wild type TLAB Embryo		Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.	Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28°C in chorions until they reached the desired stage confirmed via visual morphological staging.	genotype/variation:wild type TLAB\|developmental stage:6 somite\|hpf	GSM3084402	GSM3084402: WT zebrafish embryo 6 somite; Danio rerio; RNA Seq	GSM3084402		1	Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.	GEO Accession:GSM3084402	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP137889	dangling references:treat as unmapped	10xWT6S_possorted_genome_bam.bam	10X Genomics bam file	9353929816.0	161274652.0	GSM3084402 r1	0:58	A:2687281275;C:1909606804;G:2337322093;T:2396497626;N:23222018	58			2687281275	1909606804	2337322093	2396497626	23222018	SRX3899096	SRS3136393	SRA683448	GEO	Schier Lab, Molecular and Cellular Biology, Harvard University	1	0.94618		0.07281		0.8435		0.501		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2018-04-06	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
49405	49405	SRR7904989	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-1_S9_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L001_R2_001.fastq.gz	fastq fastq	20612658541.0	68497783.0	GSM3402061 r1	0:150.50 1:150.43	A:5839137036;C:3293726779;G:3429783599;T:8049467865;N:543262	150	150		5839137036	3293726779	3429783599	8049467865	543262	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04293	0.91361	0.0057	0.0679	0.97494	0.8187	0.48327	0.49296	150	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49406	49406	SRR7904990	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-1_S9_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L002_R2_001.fastq.gz	fastq fastq	20253907193.0	67305836.0	GSM3402061 r2	0:150.50 1:150.43	A:5762133423;C:3217021369;G:3378178325;T:7895841084;N:732992	150	150		5762133423	3217021369	3378178325	7895841084	732992	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04531	0.91352	0.006	0.06682	0.97486	0.81889	0.47811	0.50237	151	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49407	49407	SRR7904991	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-2_S10_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-2_S10_L001_R2_001.fastq.gz	fastq fastq	27785082649.0	92332127.0	GSM3402061 r3	0:150.50 1:150.43	A:7841096067;C:4446010985;G:4651723884;T:10845511192;N:740521	150	150		7841096067	4446010985	4651723884	10845511192	740521	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04331	0.91411	0.00615	0.06569	0.97445	0.81811	0.49279	0.49519	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49408	49408	SRR7904992	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-2_S10_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-2_S10_L002_R2_001.fastq.gz	fastq fastq	27318509546.0	90782131.0	GSM3402061 r4	0:150.50 1:150.43	A:7740943497;C:4344963417;G:4586054221;T:10645559884;N:988527	150	150		7740943497	4344963417	4586054221	10645559884	988527	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04427	0.91382	0.0067	0.06513	0.97591	0.82108	0.48265	0.49507	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49409	49409	SRR7904993	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-3_S11_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-3_S11_L001_R2_001.fastq.gz	fastq fastq	31234027865.0	103793392.0	GSM3402061 r5	0:150.50 1:150.42	A:8823333085;C:5009305885;G:5218885705;T:12181644470;N:858720	150	150		8823333085	5009305885	5218885705	12181644470	858720	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04428	0.91401	0.00582	0.06526	0.97386	0.81929	0.48301	0.48484	151	150	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49410	49410	SRR7904994	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-3_S11_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-3_S11_L002_R2_001.fastq.gz	fastq fastq	30613372965.0	101731210.0	GSM3402061 r6	0:150.50 1:150.43	A:8682212918;C:4881597987;G:5129046172;T:11919400304;N:1115584	150	150		8682212918	4881597987	5129046172	11919400304	1115584	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04794	0.9141	0.0063	0.06497	0.97341	0.81964	0.49569	0.48688	150	149	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49411	49411	SRR7904995	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-4_S12_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-4_S12_L001_R2_001.fastq.gz	fastq fastq	23492564280.0	78066400.0	GSM3402061 r7	0:150.50 1:150.43	A:6598565482;C:3770698909;G:3958112639;T:9164535441;N:651809	150	150		6598565482	3770698909	3958112639	9164535441	651809	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04344	0.91428	0.00609	0.06479	0.97467	0.82122	0.49508	0.49851	150	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
49412	49412	SRR7904996	SRX4741349	SRS3822681	SRP162658	PRJNA493234	Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]	GSE120503	Other	To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.	parent bioproject:PRJNA493631	pubmed:31042481;pubmed:33785593		52 hpf CHT cells	GSM3402061	tissue:zebrafish embryos\|region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	52 hpf CHT cells	UMI tools was used to analysis our single cell data. Firstly in “whitelist” step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts	zebrafish embryos		The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture’s introduction.		region:CHT\|cells:endothelial cells+hematopoietic cells+ double negative niche cells\|Stage:52 hpf	GSM3402061	GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq	GSM3402061		1	The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.	GEO Accession:GSM3402061	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP162658		171353A_zebrafish_HSC_mixture-4_S12_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-4_S12_L002_R2_001.fastq.gz	fastq fastq	23083950792.0	76709058.0	GSM3402061 r8	0:150.50 1:150.43	A:6509221386;C:3683018771;G:3901144866;T:8989732881;N:832888	150	150		6509221386	3683018771	3901144866	8989732881	832888	SRX4741349	SRS3822681	SRA784241	GEO	Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)	2	0.04694	0.91333	0.00703	0.06467	0.97447	0.82268	0.467	0.50114	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-09-26	Hatching	Embryo	Embryo Imprecise	All anatomical structures
50657	50657	SRR8206458	SRX5025783	SRS4057283	SRP169565	PRJNA506002	Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina	GSE122680	Transcriptome Analysis	It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage		pubmed:32467236		14 dpf retina rep	GSM3478019	source name:Retina\|strain:AB\|genotype:wildtype\|tissue:CMZ\|developmental stage:14 dpf	14 dpf retina rep	Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx	Retina		We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.		strain:AB\|genotype:wildtype\|tissue:CMZ\|developmental stage:14 dpf	GSM3478019	GSM3478019: 14 dpf retina rep; Danio rerio; RNA Seq	GSM3478019		1	We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.	GEO Accession:GSM3478019	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565		14dpf_rep_possorted_genome_bam.bam	10X Genomics bam file	47036574600.0	313577164.0	GSM3478019 r1	0:150	A:13973403132;C:10042891919;G:11111376691;T:11908672715;N:230143	150			13973403132	10042891919	11111376691	11908672715	230143	SRX5025783	SRS4057283	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.93407		0.06456		0.84522		0.48431		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Larval	Larval	Embryo Imprecise	All anatomical structures
50659	50659	SRR11812065	SRX5025781	SRS4057281	SRP169565	PRJNA506002	Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina	GSE122680	Transcriptome Analysis	It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage		pubmed:32467236		14 dpf retina	GSM3478017	source name:Retina\|strain:AB\|genotype:wildtype\|tissue:CMZ\|developmental stage:14 dpf	14 dpf retina	Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv genes.tsv matrix.mtx	Retina		We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer’s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer’s protocol.		strain:AB\|genotype:wildtype\|tissue:CMZ\|developmental stage:14 dpf	GSM3478017	GSM3478017: 14 dpf retina; Danio rerio; RNA Seq	GSM3478017		1	We dissected 24 36 48 72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40μm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.	GEO Accession:GSM3478017	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565	intentional duplicate	14dpf_possorted_genome_bam.bam	10X Genomics bam file	49517321418.0	342283822.0	GSM3478017 r11	0:144.67	A:14667671784;C:10143561921;G:11341438449;T:13364496000;N:153264	144			14667671784	10143561921	11341438449	13364496000	153264	SRX5025781	SRS4057281	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.88653		0.0963		0.81909		0.51027		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Larval	Larval	Embryo Imprecise	All anatomical structures
51192	51192	SRR8592248	SRX5392461	SRS4380284	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610370	tissue:control nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	control nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610370	GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610370		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L001 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L001 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L001 R2 001.fastq.gz	10X_Ctrl_uninjected_3zf_S1_L001_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L001_R2_001.fastq.gz	fastq fastq fastq	13724509526.0	75409393.0	GSM3610370 r1	0:8 1:27 2:147	A:3850897681;C:3014748648;G:3154637947;T:3685016570;N:19208680	8	27	147	3850897681	3014748648	3154637947	3685016570	19208680	SRX5392461	SRS4380284	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91575		0.07488		0.82871		0.51761		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
51193	51193	SRR8592249	SRX5392461	SRS4380284	SRP186305	PRJNA522917	Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation	GSE126647	Transcriptome Analysis	Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated few signals are understood that specifically restrict the size of the vertebrate OFT. Here we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants which lack the transcription factor Pbx4 produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors which contribute to the OFT and adjacent endothelial cell progenitors which contribute to posterior pharyngeal arch arteries. Subsequently Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior differentiated cardiomyocyte populations. Therefore the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes we utilized single cell RNA Seq scRNA Seq data sets collected from control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.		pubmed:32094112		control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610370	tissue:control nkx2.5:ZsYellow+ cells\|strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment filtering barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv Genes genes.tsv and Matrix matrix.mtx	control nkx2.5:ZsYellow+ cells		Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry		strain background:AB/TU\|age:28 hpf progenitors and cardiomyocytes\|cell type:nkx2.5:ZsYellow+ cells	GSM3610370	GSM3610370: control nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq	GSM3610370		1	Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver 2016 with the following modifications approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase Roche. Embryos were deyolked by pipetting up and down first with a p1000 tip and subsequently with a p100 tip as described by Samsa et al. 2016. Following yolk removal embryos were incubated at 32.5°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by Samsa et al. 2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry	GEO Accession:GSM3610370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP186305	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X Ctrl uninjected 3zf S1 L002 I1 001.fastq.gz read2PairFiles=10X Ctrl uninjected 3zf S1 L002 R1 001.fastq.gz read3PairFiles=10X Ctrl uninjected 3zf S1 L002 R2 001.fastq.gz	10X_Ctrl_uninjected_3zf_S1_L002_I1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R1_001.fastq.gz 10X_Ctrl_uninjected_3zf_S1_L002_R2_001.fastq.gz	fastq fastq fastq	13903413706.0	76392383.0	GSM3610370 r2	0:8 1:27 2:147	A:3900618364;C:3054470646;G:3195816893;T:3735199844;N:17307959	8	27	147	3900618364	3054470646	3195816893	3735199844	17307959	SRX5392461	SRS4380284	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91438		0.07364		0.82893		0.50278		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-02-15	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
55649	55649	SRR10611686	SRX7290958	SRS5784121	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				BP 30h	GSM4210785	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:100ppb BPA	BP 30h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:100ppb BPA	GSM4210785	GSM4210785: BP 30h; Danio rerio; RNA Seq	GSM4210785		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210785	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		BP-30h_S6_L006_R1_001.fastq.gz BP-30h_S6_L006_R2_001.fastq.gz	fastq fastq	123297367860.0	408269430.0	GSM4210785 r1	0:151 1:151	A:29612865612;C:21327621660;G:21810738134;T:50523353893;N:22788561	151	151		29612865612	21327621660	21810738134	50523353893	22788561	SRX7290958	SRS5784121	SRA1008496	GEO	Nanjing University	2	0.07493	0.92162	0.00891	0.06219	0.98299	0.81594	0.48492	0.48154	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
55650	55650	SRR10611685	SRX7290957	SRS5784120	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				BP 12h	GSM4210784	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:12hpf\|exposed pollutants:100ppb BPA	BP 12h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:12hpf\|exposed pollutants:100ppb BPA	GSM4210784	GSM4210784: BP 12h; Danio rerio; RNA Seq	GSM4210784		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210784	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		BP-12h_S4_L004_R1_001.fastq.gz BP-12h_S4_L004_R2_001.fastq.gz	fastq fastq	107141069708.0	354771754.0	GSM4210784 r1	0:151 1:151	A:26617621707;C:17860363455;G:18438338656;T:44205389572;N:19356318	151	151		26617621707	17860363455	18438338656	44205389572	19356318	SRX7290957	SRS5784120	SRA1008496	GEO	Nanjing University	2	0.08704	0.91488	0.01108	0.08743	0.98494	0.81316	0.53016	0.47931	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
55651	55651	SRR10611684	SRX7290956	SRS5784117	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				BP 8h	GSM4210783	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:100ppb BPA	BP 8h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:100ppb BPA	GSM4210783	GSM4210783: BP 8h; Danio rerio; RNA Seq	GSM4210783		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210783	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		BP-8h_S2_L002_R1_001.fastq.gz BP-8h_S2_L002_R2_001.fastq.gz	fastq fastq	112920017284.0	373907342.0	GSM4210783 r1	0:151 1:151	A:29091217868;C:18813523727;G:19294526701;T:45706210539;N:14538449	151	151		29091217868	18813523727	19294526701	45706210539	14538449	SRX7290956	SRS5784117	SRA1008496	GEO	Nanjing University	2	0.13456	0.90846	0.01758	0.09803	0.98293	0.81826	0.55099	0.50254	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
55652	55652	SRR10611683	SRX7290955	SRS5784116	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				CK 30h	GSM4210782	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:n1	CK 30h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:30hpf\|exposed pollutants:n1	GSM4210782	GSM4210782: CK 30h; Danio rerio; RNA Seq	GSM4210782		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210782	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		CK-30h_S5_L005_R1_001.fastq.gz CK-30h_S5_L005_R2_001.fastq.gz	fastq fastq	106224273812.0	351736006.0	GSM4210782 r1	0:151 1:151	A:25405444654;C:18089775514;G:18594095209;T:44115027002;N:19931433	151	151		25405444654	18089775514	18594095209	44115027002	19931433	SRX7290955	SRS5784116	SRA1008496	GEO	Nanjing University	2	0.06113	0.92264	0.00743	0.0605	0.98415	0.81675	0.50316	0.47382	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
55653	55653	SRR10611682	SRX7290954	SRS5784119	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				CK 12h	GSM4210781	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:12hpf\|exposed pollutants:n1	CK 12h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:12hpf\|exposed pollutants:n1	GSM4210781	GSM4210781: CK 12h; Danio rerio; RNA Seq	GSM4210781		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210781	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		CK-12h_S3_L003_R1_001.fastq.gz CK-12h_S3_L003_R2_001.fastq.gz	fastq fastq	104307666146.0	345389623.0	GSM4210781 r1	0:151 1:151	A:25979928759;C:17362219827;G:18048535744;T:42903273069;N:13708747	151	151		25979928759	17362219827	18048535744	42903273069	13708747	SRX7290954	SRS5784119	SRA1008496	GEO	Nanjing University	2	0.08003	0.91078	0.01149	0.08744	0.98561	0.81152	0.53825	0.48534	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
55654	55654	SRR10611681	SRX7290953	SRS5784118	SRP235262	PRJNA594336	Single cell sequencing reveals heterogeneity effects of bisphenol A on zebrafish embryonic development	GSE141664	Transcriptome Analysis	Embryonic period is sensitive window of bisphenol A BPA exposure. However embryonic development is a highly dynamic process with changing cell populations and gene expression profiles. Heterogeneity effects of BPA on fish embryonic development remain not clear. This study applied single cell RNA sequencing to analyze the impact of BPA exposure on transcriptome heterogeneity of 64683 cells from zebrafish embryos at 8 12 hpf and 30 hpf. A total of 38 cell populations were identified and gene expression profiles of 16 cell populations were significantly altered by BPA exposure. The strongest toxic effects of BPA were found at 12 hpf of segmentation stage which is an active stage of cell differentiation. At 8 hpf BPA mainly influenced the outer layer cell populations of embryos such as neural plate border and enveloping layer cells. At 12 hpf and 30 hpf nervous system formation and heart morphogenesis were disturbed. Differential process of neural plate border neural crest and neuron cells was altered leading to increased neurogenesis. For the forebrain midbrain neurons and optic cells the altered cell division and DNA replication and repair were identified. Our study for the first time provides the comprehensive understanding of BPA toxicity on fish embryo development at single cell levels. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish embryonic development following exposure to bisphenol A at different stage gastrulation segmentation and pharyngula.				CK 8h	GSM4210780	source name:zebrafish embryo\|tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:n1	CK 8h	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	zebrafish embryo	Exposure solutions were prepared by adding 100 μg/L BPA to culture medium. The exposure solution were was replaced every 12 hours.At three different stages gasturla segmentation and pharyngula zebrafish embryo were collected.	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an illumina Xten.		tissue:embryonic single cell suspension\|age:8hpf\|exposed pollutants:n1	GSM4210780	GSM4210780: CK 8h; Danio rerio; RNA Seq	GSM4210780		1	The zebrafish embryo was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an illumina Xten.	GEO Accession:GSM4210780	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP235262		CK-8h_S1_L001_R1_001.fastq.gz CK-8h_S1_L001_R2_001.fastq.gz	fastq fastq	117112087438.0	387788369.0	GSM4210780 r1	0:151 1:151	A:30237691607;C:19643608086;G:20051803632;T:47157015762;N:21968351	151	151		30237691607	19643608086	20051803632	47157015762	21968351	SRX7290953	SRS5784118	SRA1008496	GEO	Nanjing University	2	0.12513	0.90183	0.01627	0.09322	0.98255	0.81937	0.56652	0.49202	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56746	56746	SRR15813443	SRX12105547	SRS10085839	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s6	GSM5567817	tissue:wt reference hpf 10\|strain:WT\|Stage:10 hpf\|experiment:WT embryo	wt s6	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 10		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:10 hpf\|experiment:WT embryo	GSM5567817	GSM5567817: wt s6; Danio rerio; RNA Seq	GSM5567817		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567817	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s6_possorted_genome_bam.bam	10X Genomics bam file	10559763630.0	117330707.0	GSM5567817 r1	0:90	A:3140440043;C:2269672250;G:2444938588;T:2701186457;N:3526292	90			3140440043	2269672250	2444938588	2701186457	3526292	SRX12105547	SRS10085839	SRA1042742	GEO	Washington University in St Louis	1	0.91901		0.24752		0.80736		0.6329		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56747	56747	SRR15813442	SRX12105546	SRS10085840	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s5	GSM5567816	tissue:wt reference hpf 10\|strain:WT\|Stage:10 hpf\|experiment:WT embryo	wt s5	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 10		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:10 hpf\|experiment:WT embryo	GSM5567816	GSM5567816: wt s5; Danio rerio; RNA Seq	GSM5567816		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567816	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s5_possorted_genome_bam.bam	10X Genomics bam file	7404734700.0	82274830.0	GSM5567816 r1	0:90	A:2195721377;C:1607643736;G:1735950843;T:1863072717;N:2346027	90			2195721377	1607643736	1735950843	1863072717	2346027	SRX12105546	SRS10085840	SRA1042742	GEO	Washington University in St Louis	1	0.91448		0.23763		0.80933		0.63338		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56748	56748	SRR15813441	SRX12105545	SRS10085841	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s4	GSM5567815	tissue:wt reference hpf 8\|strain:WT\|Stage:8 hpf\|experiment:WT embryo	wt s4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 8		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:8 hpf\|experiment:WT embryo	GSM5567815	GSM5567815: wt s4; Danio rerio; RNA Seq	GSM5567815		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567815	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s4_possorted_genome_bam.bam	10X Genomics bam file	16164581310.0	179606459.0	GSM5567815 r1	0:90	A:4832582846;C:3490996022;G:3746675672;T:4088577265;N:5749505	90			4832582846	3490996022	3746675672	4088577265	5749505	SRX12105545	SRS10085841	SRA1042742	GEO	Washington University in St Louis	1	0.90609		0.22195		0.82085		0.64383		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56749	56749	SRR15813440	SRX12105544	SRS10085838	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s3	GSM5567814	tissue:wt reference hpf 8\|strain:WT\|Stage:8 hpf\|experiment:WT embryo	wt s3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 8		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:8 hpf\|experiment:WT embryo	GSM5567814	GSM5567814: wt s3; Danio rerio; RNA Seq	GSM5567814		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567814	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s3_possorted_genome_bam.bam	10X Genomics bam file	13357030950.0	148411455.0	GSM5567814 r1	0:90	A:3992336370;C:2912423812;G:3128958676;T:3318661163;N:4650929	90			3992336370	2912423812	3128958676	3318661163	4650929	SRX12105544	SRS10085838	SRA1042742	GEO	Washington University in St Louis	1	0.9059		0.21809		0.82578		0.64796		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56750	56750	SRR15813439	SRX12105543	SRS10085837	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s2	GSM5567813	tissue:wt reference hpf 6\|strain:WT\|Stage:6 hpf\|experiment:WT embryo	wt s2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 6		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:6 hpf\|experiment:WT embryo	GSM5567813	GSM5567813: wt s2; Danio rerio; RNA Seq	GSM5567813		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567813	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s2_possorted_genome_bam.bam	10X Genomics bam file	16886072430.0	187623027.0	GSM5567813 r1	0:90	A:4987160925;C:3716401392;G:4001055160;T:4174238739;N:7216214	90			4987160925	3716401392	4001055160	4174238739	7216214	SRX12105543	SRS10085837	SRA1042742	GEO	Washington University in St Louis	1	0.9034		0.19315		0.81038		0.65382		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56751	56751	SRR15813438	SRX12105542	SRS10085835	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		wt s1	GSM5567812	tissue:wt reference hpf 6\|strain:WT\|Stage:6 hpf\|experiment:WT embryo	wt s1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	wt reference hpf 6		10x Genomcis Chromium single cell preparation		strain:WT\|Stage:6 hpf\|experiment:WT embryo	GSM5567812	GSM5567812: wt s1; Danio rerio; RNA Seq	GSM5567812		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	wt_s1_possorted_genome_bam.bam	10X Genomics bam file	19790815230.0	219897947.0	GSM5567812 r1	0:90	A:5848816040;C:4330412374;G:4675552886;T:4927327121;N:8706809	90			5848816040	4330412374	4675552886	4927327121	8706809	SRX12105542	SRS10085835	SRA1042742	GEO	Washington University in St Louis	1	0.90894		0.18849		0.80771		0.64881		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56752	56752	SRR15813437	SRX12105541	SRS10085836	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 7	GSM5567811	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 7	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567811	GSM5567811: tyr 7; Danio rerio; RNA Seq	GSM5567811		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567811	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_7_possorted_genome_bam.bam	10X Genomics bam file	17956913490.0	199521261.0	GSM5567811 r1	0:90	A:5196658241;C:3876984519;G:4299586871;T:4578633727;N:5050132	90			5196658241	3876984519	4299586871	4578633727	5050132	SRX12105541	SRS10085836	SRA1042742	GEO	Washington University in St Louis	1	0.91768		0.22887		0.82108		0.56033		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56753	56753	SRR15813436	SRX12105540	SRS10085834	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 6	GSM5567810	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 6	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567810	GSM5567810: tyr 6; Danio rerio; RNA Seq	GSM5567810		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567810	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_6_possorted_genome_bam.bam	10X Genomics bam file	20779298370.0	230881093.0	GSM5567810 r1	0:90	A:5921943503;C:4559349693;G:5076139988;T:5215980107;N:5885079	90			5921943503	4559349693	5076139988	5215980107	5885079	SRX12105540	SRS10085834	SRA1042742	GEO	Washington University in St Louis	1	0.92027		0.21718		0.82558		0.55659		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56754	56754	SRR15813435	SRX12105539	SRS10085833	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 5	GSM5567809	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 5	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567809	GSM5567809: tyr 5; Danio rerio; RNA Seq	GSM5567809		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567809	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_5_possorted_genome_bam.bam	10X Genomics bam file	11100581280.0	123339792.0	GSM5567809 r1	0:90	A:3139119132;C:2435865589;G:2721973969;T:2802951898;N:670692	90			3139119132	2435865589	2721973969	2802951898	670692	SRX12105539	SRS10085833	SRA1042742	GEO	Washington University in St Louis	1	0.93417		0.15847		0.83347		0.5442		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56755	56755	SRR15813434	SRX12105538	SRS10085832	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 4	GSM5567808	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567808	GSM5567808: tyr 4; Danio rerio; RNA Seq	GSM5567808		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567808	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_4_possorted_genome_bam.bam	10X Genomics bam file	12537663570.0	139307373.0	GSM5567808 r1	0:90	A:3622205893;C:2682389272;G:2969276928;T:3261280923;N:2510554	90			3622205893	2682389272	2969276928	3261280923	2510554	SRX12105538	SRS10085832	SRA1042742	GEO	Washington University in St Louis	1	0.93183		0.17593		0.82674		0.54339		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56756	56756	SRR15813433	SRX12105537	SRS10085831	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 3	GSM5567807	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567807	GSM5567807: tyr 3; Danio rerio; RNA Seq	GSM5567807		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567807	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_3_possorted_genome_bam.bam	10X Genomics bam file	14347674270.0	159418603.0	GSM5567807 r1	0:90	A:4145829296;C:3058277848;G:3413742462;T:3725775591;N:4049073	90			4145829296	3058277848	3413742462	3725775591	4049073	SRX12105537	SRS10085831	SRA1042742	GEO	Washington University in St Louis	1	0.92892		0.16288		0.82724		0.52654		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56757	56757	SRR15813432	SRX12105536	SRS10085830	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 2	GSM5567806	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567806	GSM5567806: tyr 2; Danio rerio; RNA Seq	GSM5567806		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567806	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_2_possorted_genome_bam.bam	10X Genomics bam file	10069177770.0	111879753.0	GSM5567806 r1	0:90	A:2905395164;C:2177772281;G:2406688540;T:2577323490;N:1998295	90			2905395164	2177772281	2406688540	2577323490	1998295	SRX12105536	SRS10085830	SRA1042742	GEO	Washington University in St Louis	1	0.92725		0.19411		0.831		0.57759		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56758	56758	SRR15813431	SRX12105535	SRS10085829	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		tyr 1	GSM5567805	tissue:tyr crispant\|strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	tyr 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	tyr crispant		10x Genomcis Chromium single cell preparation		strain:tyr crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567805	GSM5567805: tyr 1; Danio rerio; RNA Seq	GSM5567805		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567805	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	tyr_1_possorted_genome_bam.bam	10X Genomics bam file	13916932740.0	154632586.0	GSM5567805 r1	0:90	A:4011009499;C:3001925064;G:3335796140;T:3563954880;N:4247157	90			4011009499	3001925064	3335796140	3563954880	4247157	SRX12105535	SRS10085829	SRA1042742	GEO	Washington University in St Louis	1	0.92833		0.18624		0.82584		0.55384		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56759	56759	SRR15813430	SRX12105534	SRS10085828	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		sebox 3	GSM5567804	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567804	GSM5567804: sebox 3; Danio rerio; RNA Seq	GSM5567804		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567804	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_3_possorted_genome_bam.bam	10X Genomics bam file	15063590430.0	167373227.0	GSM5567804 r1	0:90	A:4342780592;C:3200398068;G:3565351581;T:3953977957;N:1082232	90			4342780592	3200398068	3565351581	3953977957	1082232	SRX12105534	SRS10085828	SRA1042742	GEO	Washington University in St Louis	1	0.92955		0.17763		0.82382		0.5348		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56760	56760	SRR15813429	SRX12105533	SRS10085827	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		sebox 2	GSM5567803	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567803	GSM5567803: sebox 2; Danio rerio; RNA Seq	GSM5567803		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567803	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_2_possorted_genome_bam.bam	10X Genomics bam file	10155028230.0	112833647.0	GSM5567803 r1	0:90	A:2847715131;C:2249340222;G:2497174890;T:2560077085;N:720902	90			2847715131	2249340222	2497174890	2560077085	720902	SRX12105533	SRS10085827	SRA1042742	GEO	Washington University in St Louis	1	0.9413		0.17155		0.83236		0.5478		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56761	56761	SRR15813428	SRX12105532	SRS10085826	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		sebox 1	GSM5567802	tissue:sebox crispant\|strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	sebox 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	sebox crispant		10x Genomcis Chromium single cell preparation		strain:sebox crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567802	GSM5567802: sebox 1; Danio rerio; RNA Seq	GSM5567802		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567802	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	sebox_1_possorted_genome_bam.bam	10X Genomics bam file	15631632990.0	173684811.0	GSM5567802 r1	0:90	A:4504570341;C:3335848026;G:3720024502;T:4070070942;N:1119179	90			4504570341	3335848026	3720024502	4070070942	1119179	SRX12105532	SRS10085826	SRA1042742	GEO	Washington University in St Louis	1	0.91841		0.19		0.82367		0.54474		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56762	56762	SRR15813427	SRX12105531	SRS10085825	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		noto 3	GSM5567801	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567801	GSM5567801: noto 3; Danio rerio; RNA Seq	GSM5567801		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567801	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_3_possorted_genome_bam.bam	10X Genomics bam file	9696476250.0	107738625.0	GSM5567801 r1	0:90	A:2759552091;C:2046867650;G:2381514508;T:2503080064;N:5461937	90			2759552091	2046867650	2381514508	2503080064	5461937	SRX12105531	SRS10085825	SRA1042742	GEO	Washington University in St Louis	1	0.88572		0.24263		0.83228		0.5118		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56763	56763	SRR15813426	SRX12105530	SRS10085824	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		noto 2	GSM5567800	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567800	GSM5567800: noto 2; Danio rerio; RNA Seq	GSM5567800		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567800	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_2_possorted_genome_bam.bam	10X Genomics bam file	6805896120.0	75621068.0	GSM5567800 r1	0:90	A:1937849673;C:1444333862;G:1669710397;T:1750230467;N:3771721	90			1937849673	1444333862	1669710397	1750230467	3771721	SRX12105530	SRS10085824	SRA1042742	GEO	Washington University in St Louis	1	0.88304		0.22942		0.82958		0.50945		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56764	56764	SRR15813425	SRX12105529	SRS10085822	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		noto 1	GSM5567799	tissue:noto crispant\|strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	noto 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	noto crispant		10x Genomcis Chromium single cell preparation		strain:noto crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567799	GSM5567799: noto 1; Danio rerio; RNA Seq	GSM5567799		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567799	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	noto_1_possorted_genome_bam.bam	10X Genomics bam file	7424025120.0	82489168.0	GSM5567799 r1	0:90	A:2111968765;C:1577509540;G:1827370183;T:1903046323;N:4130309	90			2111968765	1577509540	1827370183	1903046323	4130309	SRX12105529	SRS10085822	SRA1042742	GEO	Washington University in St Louis	1	0.86603		0.22594		0.83073		0.51508		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56765	56765	SRR15813424	SRX12105528	SRS10085823	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		lhx1a 4	GSM5567798	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 4	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567798	GSM5567798: lhx1a 4; Danio rerio; RNA Seq	GSM5567798		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567798	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_4_possorted_genome_bam.bam	10X Genomics bam file	22087787670.0	245419863.0	GSM5567798 r1	0:90	A:6475797345;C:4735192179;G:5275258568;T:5599207862;N:2331716	90			6475797345	4735192179	5275258568	5599207862	2331716	SRX12105528	SRS10085823	SRA1042742	GEO	Washington University in St Louis	1	0.91015		0.22744		0.83278		0.55743		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56766	56766	SRR15813423	SRX12105527	SRS10085820	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		lhx1a 3	GSM5567797	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567797	GSM5567797: lhx1a 3; Danio rerio; RNA Seq	GSM5567797		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567797	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_3_possorted_genome_bam.bam	10X Genomics bam file	20620567800.0	229117420.0	GSM5567797 r1	0:90	A:5887591442;C:4508984476;G:5046355704;T:5175484329;N:2151849	90			5887591442	4508984476	5046355704	5175484329	2151849	SRX12105527	SRS10085820	SRA1042742	GEO	Washington University in St Louis	1	0.92195		0.22061		0.83224		0.56225		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56767	56767	SRR15813422	SRX12105526	SRS10085821	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		lhx1a 2	GSM5567796	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567796	GSM5567796: lhx1a 2; Danio rerio; RNA Seq	GSM5567796		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567796	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_2_possorted_genome_bam.bam	10X Genomics bam file	9946966230.0	110521847.0	GSM5567796 r1	0:90	A:2788146910;C:2206643231;G:2469755316;T:2481819884;N:600889	90			2788146910	2206643231	2469755316	2481819884	600889	SRX12105526	SRS10085821	SRA1042742	GEO	Washington University in St Louis	1	0.91371		0.24403		0.82629		0.58866		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56768	56768	SRR15813421	SRX12105525	SRS10085819	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		lhx1a 1	GSM5567795	tissue:lhx1a crispant\|strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	lhx1a 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	lhx1a crispant		10x Genomcis Chromium single cell preparation		strain:lhx1a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567795	GSM5567795: lhx1a 1; Danio rerio; RNA Seq	GSM5567795		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567795	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	lhx1a_1_possorted_genome_bam.bam	10X Genomics bam file	19493469630.0	216594107.0	GSM5567795 r1	0:90	A:5626093917;C:4175669632;G:4665965196;T:5024562911;N:1177974	90			5626093917	4175669632	4665965196	5024562911	1177974	SRX12105525	SRS10085819	SRA1042742	GEO	Washington University in St Louis	1	0.90552		0.2132		0.81921		0.56307		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56769	56769	SRR15813420	SRX12105524	SRS10085818	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		irx3a 3	GSM5567794	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 3	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567794	GSM5567794: irx3a 3; Danio rerio; RNA Seq	GSM5567794		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567794	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_3_possorted_genome_bam.bam	10X Genomics bam file	8702629560.0	96695884.0	GSM5567794 r1	0:90	A:2502778147;C:1869454970;G:2100874536;T:2226298889;N:3223018	90			2502778147	1869454970	2100874536	2226298889	3223018	SRX12105524	SRS10085818	SRA1042742	GEO	Washington University in St Louis	1	0.93135		0.17699		0.83031		0.56065		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56770	56770	SRR15813419	SRX12105523	SRS10085814	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		irx3a 2	GSM5567793	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 2	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567793	GSM5567793: irx3a 2; Danio rerio; RNA Seq	GSM5567793		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567793	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_2_possorted_genome_bam.bam	10X Genomics bam file	13516567200.0	150184080.0	GSM5567793 r1	0:90	A:3934125495;C:2881926208;G:3210954290;T:3485647605;N:3913602	90			3934125495	2881926208	3210954290	3485647605	3913602	SRX12105523	SRS10085814	SRA1042742	GEO	Washington University in St Louis	1	0.92263		0.18193		0.8267		0.55492		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
56771	56771	SRR15813418	SRX12105522	SRS10085815	SRP249509	PRJNA606682	CellOracle: Dissecting cell identity via network inference and in silico gene perturbation	GSE145298	Other	Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.		pubmed:36755098		irx3a 1	GSM5567792	tissue:irx3a crispant\|strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	irx3a 1	Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz	irx3a crispant		10x Genomcis Chromium single cell preparation		strain:irx3a crispant generated from wild type\|Stage:10 hpf\|experiment:Cas9 and gRNA Ribonucleoprotein complex is injected to hpf 0 zebrafish embryo	GSM5567792	GSM5567792: irx3a 1; Danio rerio; RNA Seq	GSM5567792		1	10x Genomcis Chromium single cell preparation	GEO Accession:GSM5567792	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249509	assembly:GRCz11\|intentional duplicate	irx3a_1_possorted_genome_bam.bam	10X Genomics bam file	14095641960.0	156618244.0	GSM5567792 r1	0:90	A:4094793830;C:2977588403;G:3309296706;T:3709972016;N:3991005	90			4094793830	2977588403	3309296706	3709972016	3991005	SRX12105522	SRS10085815	SRA1042742	GEO	Washington University in St Louis	1	0.93495		0.16833		0.82505		0.54259		90		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-09-08	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
61425	61425	SRR12749598	SRX9221555	SRS7455256	SRP285948	PRJNA666689	Spatio temporal mRNA tracking in the early zebrafish embryo	GSE158849	Other	We performed spatially resolved transcriptomics with sub single cell resolution in zebrafish embryos at the one cell stage which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac the vegetal pole. The three prime UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells. Overall design: Spatial transcriptomic data tomo seq from zebrafish one cell stage embroys mature X. laevis and X. tropicalis oocytes. Single cell metabolic labeling scSLAM seq of zebrafish embryos at 6 hpf.		pubmed:34099733		scSLAM seq replicate 1	GSM4812182	tissue:shield stage embryos 6 hpf\|strain:AB wildtype\|treatment:4sUTP injected\|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome.	scSLAM seq replicate 1	zebrafish tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode Genome build: GRCz10 release 90 Supplementary files format and content: csv file containing gene counts per section xenopus tomo seq demultiplexing with bcl2fastq v2.18.0.12 mapping with STAR v2.5.3a split counts by section barcode and translate gene identifier to gene names Genome build: X. tropicalis v9.1 genome assembly X.laevis v9.2 genome assembly Supplementary files format and content: csv file containing gene counts per section scSLAM seq zebrafish demultiplexing using cellranger mkfastq v3.0.2 mapping and whitelisting of cells with cellranger v3.0.2 splitting labeled reads >1 T C mutation from unlabeled into separate fastq files submitted to this GEO entry mapping with STARsolo v2.7.0f 0328 single cell analysis in seurat v3.1.2 Genome build: GRCz11 Supplementary files format and content: barcodes.tsv list of barcodes genes.tsv list of genes and matrix.tsv count matrix	shield stage embryos 6 hpf		none provided by the submitter		strain:AB wildtype\|treatment:4sUTP injected\|extraction protocol:Methanol fixed single cell suspension 10x Genomics transcriptome.	GSM4812182	GSM4812182: scSLAM seq replicate 1; Danio rerio; RNA Seq	GSM4812182		1	none provided by the submitter	GEO Accession:GSM4812182	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP285948		scSLAMseq.zebrafish.6hpf.R1.fastq.gz scSLAMseq.zebrafish.6hpf.R2.fastq.gz	fastq fastq	18763873688.0	151321562.0	GSM4812182 r1	0:26 1:98	A:5330726187;C:3994611684;G:4055930332;T:5373535151;N:9070334	26	98		5330726187	3994611684	4055930332	5373535151	9070334	SRX9221555	SRS7455256	SRA1136461	GEO	Junker, BIMSB, MDC	2	0.00126	0.81459	0.0004	0.05503	0.99717	0.82674	0.52121	0.58038	26	98	T	B	sc-like readlen	illumina	hiseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2020-09-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
61615	61615	SRR12888601	SRX9353789	SRS7576887	SRP288474	PRJNA671679	Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia	GSE160038	Transcriptome Analysis	Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.				UPEC injected 5 dpf embryo cells	GSM4855812	source name:5 dpf embryo\|tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:UPEC	UPEC injected 5 dpf embryo cells	CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell	5 dpf embryo	Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C.	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.		tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:UPEC	GSM4855812	GSM4855812: UPEC injected 5 dpf embryo cells; Danio rerio; RNA Seq	GSM4855812		1	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.	GEO Accession:GSM4855812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP288474	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Upec S4 L001 I1 001.fastq.gz read2PairFiles=Upec S4 L001 R1 001.fastq.gz read3PairFiles=Upec S4 L001 R2 001.fastq.gz	Upec_S4_L001_I1_001.fastq.gz Upec_S4_L001_R1_001.fastq.gz Upec_S4_L001_R2_001.fastq.gz	fastq fastq fastq	30696246075.0	241702725.0	GSM4855812 r1	0:8 1:28 2:91	A:8297484773;C:7271108187;G:7092330543;T:8034542269;N:780303	8	28	91	8297484773	7271108187	7092330543	8034542269	780303	SRX9353789	SRS7576887	SRA1147613	GEO	Pediatric Nephrology, Indiana University School of Medicine	1	0.94674		0.11144		0.79107		0.5211		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2020-10-25	Larval	Larval	Embryo Imprecise	All anatomical structures
61616	61616	SRR12888602	SRX9353789	SRS7576887	SRP288474	PRJNA671679	Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia	GSE160038	Transcriptome Analysis	Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.				UPEC injected 5 dpf embryo cells	GSM4855812	source name:5 dpf embryo\|tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:UPEC	UPEC injected 5 dpf embryo cells	CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell	5 dpf embryo	Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C.	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.		tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:UPEC	GSM4855812	GSM4855812: UPEC injected 5 dpf embryo cells; Danio rerio; RNA Seq	GSM4855812		1	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.	GEO Accession:GSM4855812	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP288474	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Upec S4 L002 I1 001.fastq.gz read2PairFiles=Upec S4 L002 R1 001.fastq.gz read3PairFiles=Upec S4 L002 R2 001.fastq.gz	Upec_S4_L002_I1_001.fastq.gz Upec_S4_L002_R1_001.fastq.gz Upec_S4_L002_R2_001.fastq.gz	fastq fastq fastq	30699748481.0	241730303.0	GSM4855812 r2	0:8 1:28 2:91	A:8297276041;C:7272515125;G:7096736242;T:8032333424;N:887649	8	28	91	8297276041	7272515125	7096736242	8032333424	887649	SRX9353789	SRS7576887	SRA1147613	GEO	Pediatric Nephrology, Indiana University School of Medicine	1	0.94592		0.11122		0.79141		0.51239		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2020-10-25	Larval	Larval	Embryo Imprecise	All anatomical structures
61617	61617	SRR12888599	SRX9353788	SRS7576886	SRP288474	PRJNA671679	Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia	GSE160038	Transcriptome Analysis	Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.				Saline injected 5 dpf embryo cells	GSM4855811	source name:5 dpf embryo\|tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:Saline	Saline injected 5 dpf embryo cells	CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell	5 dpf embryo	Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C.	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.		tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:Saline	GSM4855811	GSM4855811: Saline injected 5 dpf embryo cells; Danio rerio; RNA Seq	GSM4855811		1	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.	GEO Accession:GSM4855811	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP288474	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Saline S3 L001 I1 001.fastq.gz read2PairFiles=Saline S3 L001 R1 001.fastq.gz read3PairFiles=Saline S3 L001 R2 001.fastq.gz	Saline_S3_L001_I1_001.fastq.gz Saline_S3_L001_R1_001.fastq.gz Saline_S3_L001_R2_001.fastq.gz	fastq fastq fastq	35322876649.0	278132887.0	GSM4855811 r1	0:8 1:28 2:91	A:9928433363;C:8021179562;G:8210286510;T:9162083865;N:893349	8	28	91	9928433363	8021179562	8210286510	9162083865	893349	SRX9353788	SRS7576886	SRA1147613	GEO	Pediatric Nephrology, Indiana University School of Medicine	1	0.93984		0.12389		0.81724		0.46893		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2020-10-25	Larval	Larval	Embryo Imprecise	All anatomical structures
61618	61618	SRR12888600	SRX9353788	SRS7576886	SRP288474	PRJNA671679	Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia	GSE160038	Transcriptome Analysis	Urinary tract infections UTIs are the second most common infections encountered in the pediatric population second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10 30% of septic shock cases and Uropathogenic E.coli UPEC is responsible for almost 75% of cases. Therefore increased understanding of the effects of urosepsis at the cellular and organ specific level will provide the foundation for improvements in clinical care. Overall design: Two zebrafish cohorts were injected with either sterile saline or UPEC and subjected to scRNA seq. Cell clusters were identified and subjected to RNA velocity analysis. Selected clusters relevant to the innate immune system and bactericidal activity underwent canonical pathway analysis. RNA velocity analysis revealed several key changes in the transcriptional state of UPEC infected cells and pathway analysis provided key information regarding changes in innate immune pathways within the cell clusters.				Saline injected 5 dpf embryo cells	GSM4855811	source name:5 dpf embryo\|tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:Saline	Saline injected 5 dpf embryo cells	CellRanger version 3.1 was utilized to process the raw sequence data generated by the sequencer. CellRanger uses bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample specific FASTQ files The FASTQ files were then aligned to the zebrafish reference genome Danio rerio.GRCz11 with RNAseq aligner STAR The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs unique molecular indices detected in each cell.The filtered feature cell barcode matrices generated by CellRanger were used for further analysis. Genome build: GRCz11 3.1.0 Supplementary files format and content: Tab delimited text file containing count matrix for each gene and cell	5 dpf embryo	Zebrafish were injected with red fluorescent protein RFP expressing UPEC. post 24 hours the zebrafish were dissociated and then homogenate was placed on a glass slide and evaluated for RFP expression on Keyence BZII microscope. Allowed embryos to mature for 4 dpf dpf in a 28.5°C incubator in egg water filled petri dishes. Embryos were collected via visualization through dissecting microscope and separated into control and experimental groups each containing about 30 embryos. The embryos were anesthetized with tricaine and immobilized in methylcellulose. A mixture of the bacterial solution described above phenol red and PBS was made.The mixture was loaded into microneedle and about 1nl of the mixture was injected into the pericardial cavity of each embryo in the experimental group. The control group was injected with 1nl of phenol red and PBS. The embryos were then incubated for 24 hours at 28.5°C.	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.		tissue preparation:Single cell suspension\|tissue:embryo\|age:5 days\|treatment:Saline	GSM4855811	GSM4855811: Saline injected 5 dpf embryo cells; Danio rerio; RNA Seq	GSM4855811		1	The embryos were euthanized with tricaine and ice added to egg water. The embryos were then added to methylcellulose and the heads of the embryos were removed using a straight blade sterile scalpel. The remaining portion of the embryos were collected and washed 2x with cold PBS at 700g for 5 min then dissociated with Liberase TL Sigma containing DNAse I Sigma in DMEM using gentleMACS Miltenyi Biotec in C tubes then cells were incubated at 370C for 10 minutes with continuous monitoring. When cell homogenate started to disappear DMEM containing 10% FBS was added to stop the dissociation reaction. Cells were then filtered on 70µm filter and centrifuged at 1500 rpm for 10 min. Cells were counted on hemocytometer then dead cells were removed using dead cell removal microbead Miltenyi Biotec with MS column. Live cells were then centrifuged and resuspended in DPBS without xxx+ or Mg2+ and processed for single cell RNA sequencing on 10x genomics platform. Library preparation was performed usingChromium™ Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1.	GEO Accession:GSM4855811	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP288474	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=Saline S3 L002 I1 001.fastq.gz read2PairFiles=Saline S3 L002 R1 001.fastq.gz read3PairFiles=Saline S3 L002 R2 001.fastq.gz	Saline_S3_L002_I1_001.fastq.gz Saline_S3_L002_R1_001.fastq.gz Saline_S3_L002_R2_001.fastq.gz	fastq fastq fastq	35322228695.0	278127785.0	GSM4855811 r2	0:8 1:28 2:91	A:9930368061;C:8021036700;G:8212298286;T:9157497631;N:1028017	8	28	91	9930368061	8021036700	8212298286	9157497631	1028017	SRX9353788	SRS7576886	SRA1147613	GEO	Pediatric Nephrology, Indiana University School of Medicine	1	0.93844		0.1252		0.8185		0.47714		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	India	2020-10-25	Larval	Larval	Embryo Imprecise	All anatomical structures
62678	62678	SRR13302564	SRX9731496	SRS7924278	SRP299270	PRJNA687691	The alx3 gene functions to regulate skeletal cell differentiation timing during zebrafish neurocranium development.	GSE163826	Other	During craniofacial development different populations of cartilage and bone forming cells develop in precise locations in the head. Most of these cells are derived from pluripotent cranial neural crest cells. The mechanisms that divide neural crest cells into distinct populations are not fully understood. Here we use single cell RNA sequencing to transcriptomically define different populations of cranial neural crest cells. We discovered that the transcription factor encoding alx gene family is restricted to the frontonasal population of neural crest cells. Furthermore genetic mutant analyses indicate that alx3 functions to subdivide the frontonasal population into medial versus lateral subpopulations. Our results support a mechanism in which the alx gene family functions as an identity code subdividing frontonasal neural crest cells into distinct subpopulations. This study furthers our understanding of how different skeletal cell fates are established during craniofacial development and how these mechanisms can go awry in genetic diseases. Overall design: neural crest cell profiling of 24 hpf WT D. rerio		pubmed:33741714;pubmed:36134886		WT rep 1	GSM4988014	tissue:Nerual crest cells\|tissue source:neuroectoderm\|strain:AB strain\|age:24 hpf	WT rep 1	make ref / make fastq files / aggr command / count command; CellRanger 2.2.0 merge WT and mut data; Seurat v2; e10x < MergeSeuratobject1 = wt object2 = mut project = "n10x" min.cells = 5 min.genes = 100 filter for <250 genes per cell and for any mitochondrial UMIs at less than or equal to 2.5% per cell; Seurat v2; e10x < FilterCellsobject = e10x subset.names = c"nGene" "percent.mito" low.thresholds = c250 Inf high.thresholds = cInf 0.025 cluster projection/dim red. Via PCA/UMAP post WT subset; Seurat v2; nichols TSNE < RunTSNEnichols dr seurat WT dims.use = 1:10 do.fast= TRUE seed.use = 123/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE/nichols umap clusters < FindClustersobject = nichols TSNE reduction.type = "pca" dims.use = 1:15 resolution = 0.2 save.SNN = TRUE n.start = 10 nn.eps = 0.5 print.output = FALSE force.recalc = TRUE main dim reduction plot; Seurat v2; DimPlotobject = nichols umap clusters reduction.use = "umap" do.return = TRUE pt.size = 1.3 differential expression marker gene ID/localization of expression; Seurat v2; nichols umap.markers1 < FindAllMarkersnichols umap clusters only.pos = TRUE min.pct = 0.1 thresh.use = 0.25/FeaturePlot organizing genes by descending ascending pct.2; Seurat v2; subset based on ascending pct.2 visualize distribution of alx genes across each cluster; Seurat v2; VlnPlotnichols umap clusters features.plot = <each alx gene> single.legend = TRUE y.max = 2 + ggplot2::theme classic + ylab"Expression Level log TPM" pseudotemporal and lineage tracing analyses; mnonocle3 v3; Follows from pseudotime and lineage trajectory mapping vignette for Monocle 3 Trapnell et al. 2014 seurat /featureplot app; Seurat v2 RShiny; FeaturePlotnichols umap clusters diet features = input$gene name reduction = "umap" cols = c"grey" "blue" label = TRUE label.size = 4.5 pt.size = 1.5 ncol = 3 + xlim 1…	Nerual crest cells	Crispr/cas9 mutagenesis of alx3 gene Jao et al. 2013 Barske et al. 2016	32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries	Animals were maintained and staged according to established protocols Westerfield 1993 Kimmel et al. 1995.	tissue source:neuroectoderm\|strain:AB strain\|age:24 hpf	GSM4988014	GSM4988014: WT rep 1; Danio rerio; RNA Seq	GSM4988014		1	32 double transgenic flia:EGFP;sox10:mRFP embryos were dissociated into single cell suspension using cold active protease from Bacillus licheniformis DNase EDTA and trituration Adam et al. 2017 10X Genomics libraries	GEO Accession:GSM4988014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP299270		2_mef_wt_High_24hpf_R1_001.fastq.gz 2_mef_wt_High_24hpf_R2_001.fastq.gz	fastq fastq	233119629204.0	771919302.0	GSM4988014 r1	0:151 1:151	A:69457580771;C:37624255978;G:33980317215;T:87522302829;N:4535172411	151	151		69457580771	37624255978	33980317215	87522302829	4535172411	SRX9731496	SRS7924278	SRA1177732	GEO	Nichols Lab, Craniofacial Biology, University of Colorado - Anschutz Medical Campus	2	0.05174	0.87764	0.00382	0.06802	0.98435	0.84443	0.4489	0.49905	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-12-24	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
62848	62848	SRR13402902	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336	tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP301260	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L001 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L001 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L001 R2 001.fastq.gz	GUG739A4_S2_L001_I1_001.fastq.gz GUG739A4_S2_L001_R1_001.fastq.gz GUG739A4_S2_L001_R2_001.fastq.gz	fastq fastq fastq	5235400170.0	24930477.0	GSM5014336 r1	0:8 1:101 2:101	A:1177347684;C:925887308;G:939712357;T:2191666659;N:786162	8	101	101	1177347684	925887308	939712357	2191666659	786162	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.91081		0.11647		0.78459		0.5629		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures
62849	62849	SRR13402903	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336	tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP301260	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L002 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L002 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L002 R2 001.fastq.gz	GUG739A4_S2_L002_I1_001.fastq.gz GUG739A4_S2_L002_R1_001.fastq.gz GUG739A4_S2_L002_R2_001.fastq.gz	fastq fastq fastq	5543517210.0	26397701.0	GSM5014336 r2	0:8 1:101 2:101	A:1240643673;C:980694158;G:992958309;T:2328732820;N:488250	8	101	101	1240643673	980694158	992958309	2328732820	488250	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.91665		0.11529		0.78472		0.58007		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures
62850	62850	SRR13402904	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336	tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP301260	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L003 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L003 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L003 R2 001.fastq.gz	GUG739A4_S2_L003_I1_001.fastq.gz GUG739A4_S2_L003_R1_001.fastq.gz GUG739A4_S2_L003_R2_001.fastq.gz	fastq fastq fastq	5572550130.0	26535953.0	GSM5014336 r3	0:8 1:101 2:101	A:1249457035;C:994601699;G:1005584984;T:2322470542;N:435870	8	101	101	1249457035	994601699	1005584984	2322470542	435870	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.90814		0.11693		0.78565		0.57928		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures
62851	62851	SRR13402905	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336	tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP301260	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L004 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L004 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L004 R2 001.fastq.gz	GUG739A4_S2_L004_I1_001.fastq.gz GUG739A4_S2_L004_R1_001.fastq.gz GUG739A4_S2_L004_R2_001.fastq.gz	fastq fastq fastq	5614329210.0	26734901.0	GSM5014336 r4	0:8 1:101 2:101	A:1257192667;C:993041786;G:1007516062;T:2349738132;N:6840563	8	101	101	1257192667	993041786	1007516062	2349738132	6840563	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.91345		0.11553		0.78632		0.58232		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures
62852	62852	SRR13402906	SRX9821929	SRS8004722	SRP301260	PRJNA691237	Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways	GSE164574	Other	The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage		pubmed:34737283		Zsphere scRNA	GSM5014336	tissue:Zebrafish embryos\|Stage:sphere	Zsphere scRNA	We used cell ranger version 2.1.1 to deconvolve align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix features and barcode data	Zebrafish embryos		At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	Zebrafish embryos were grown in embryo media for dissection of the blastula cup embryos were transferred in DMEM F12 media	Stage:sphere	GSM5014336	GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq	GSM5014336		1	At high stage embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to 20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime	GEO Accession:GSM5014336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP301260	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=GUG739A4 S2 L005 I1 001.fastq.gz read2PairFiles=GUG739A4 S2 L005 R1 001.fastq.gz read3PairFiles=GUG739A4 S2 L005 R2 001.fastq.gz	GUG739A4_S2_L005_I1_001.fastq.gz GUG739A4_S2_L005_R1_001.fastq.gz GUG739A4_S2_L005_R2_001.fastq.gz	fastq fastq fastq	5660581290.0	26955149.0	GSM5014336 r5	0:8 1:101 2:101	A:1268509148;C:1023948185;G:1033027319;T:2334888489;N:208149	8	101	101	1268509148	1023948185	1033027319	2334888489	208149	SRX9821929	SRS8004722	SRA1182478	GEO	Bioinformatics, Bioinformatics, The Francis Crick Institute	1	0.91009		0.11843		0.78599		0.57826		101		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-01-11	Blastula	Embryo	Embryo Imprecise	All anatomical structures

Advanced export

JSON shape: default, array, newline-delimited

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");;