metadata: run_metadata: 404 rows where devstage_curation = "Hatching" and technology = "10x"

404 rows where devstage_curation = "Hatching" and technology = "10x"

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.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
15009	15009	ERR12306826	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10050750400.0	62817190.0	E MTAB 13554:230324 Coated S1 L003	0:10 1:10 2:30 3:110	A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364	10	10	30	110	1894211982	1556769050	1595134885	1863244619	530364	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15010	15010	ERR12306829	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz	fastq fastq fastq fastq	9780757760.0	61129736.0	E MTAB 13554:230324 Coated S1 L004	0:10 1:10 2:30 3:110	A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004	10	10	30	110	1844808667	1516149264	1549838165	1813091860	383004	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15011	15011	ERR12306828	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9639368480.0	60246053.0	E MTAB 13554:230324 Coated S1 L002	0:10 1:10 2:30 3:110	A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820	10	10	30	110	1817388578	1494319441	1527564319	1787447672	345820	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15012	15012	ERR12306832	ERX11683773	ERS17043893	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Coated	SAMEA114641726	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641726\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Coated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Coated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Coated p	Coated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9823147840.0	61394674.0	E MTAB 13554:230324 Coated S1 L001	0:10 1:10 2:30 3:110	A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191	10	10	30	110	1851113558	1521671335	1558230628	1822067428	331191	ERX11683773	ERS17043893	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15013	15013	ERR12306833	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	8871716800.0	55448230.0	E MTAB 13554:230324 Uncoated S2 L001	0:10 1:10 2:30 3:110	A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567	10	10	30	110	1718985845	1319560520	1372197713	1688254655	306567	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15014	15014	ERR12306830	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz	fastq fastq fastq fastq	9075478720.0	56721742.0	E MTAB 13554:230324 Uncoated S2 L003	0:10 1:10 2:30 3:110	A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625	10	10	30	110	1758677834	1349774831	1404463433	1725994897	480625	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15015	15015	ERR12306831	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8705210880.0	54407568.0	E MTAB 13554:230324 Uncoated S2 L002	0:10 1:10 2:30 3:110	A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916	10	10	30	110	1687330583	1295837902	1345522657	1655826422	314916	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
15016	15016	ERR12306827	ERX11683774	ERS17043894	ERP155237	PRJEB70303	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E-MTAB-13554	Transcriptome Analysis	To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule but containing a detection fluorophores. post treatment the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30		Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.	Uncoated	SAMEA114641727	KIS	ENA first public:2024 09 30\|External Id:SAMEA114641727\|INSDC center name:KIS\|INSDC last update:2023 11 20T16:06:50Z\|INSDC status:public\|Submitter Id:E MTAB 13554:Uncoated\|age:2\|broker name:ArrayExpress\|collection date:not collected\|common name:zebrafish\|developmental stage:embryo stage\|geographic location country and/or sea:not collected\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 13554:Uncoated\|scientific name:Danio rerio\|sex:not available\|strain:transgenic lines Tgfli1:EGFPy1									10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	E MTAB 13554:Uncoated p	Uncoated p	10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min washed once in 1X PBS filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222 transferred onto an agarose surface placed on their ventral side and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	PolyA	PAIRED	ILLUMINA	NextSeq 550	ERP155237	NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets	ENA FIRST PUBLIC:2024 09 30\|ENA LAST UPDATE:2024 09 30	230324-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz	fastq fastq fastq fastq	8846203360.0	55288771.0	E MTAB 13554:230324 Uncoated S2 L004	0:10 1:10 2:30 3:110	A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082	10	10	30	110	1715100047	1316853239	1367208350	1682248092	355082	ERX11683774	ERS17043894	ERA27417303	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B		usable mapping rate	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-11-20	Hatching	Embryo	Whole Organism	All anatomical structures
24838	24838	SRR25509990	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S65_L001_I1_001.fastq.gz Kristen_10X_101620_S65_L001_R1_001.fastq.gz Kristen_10X_101620_S65_L001_R2_001.fastq.gz	fastq fastq fastq	3327423622.0	26200186.0	GSM7680082 r1	0:8 1:28 2:91	A:693698335;C:494975421;G:540414923;T:654926705;N:201542	8	28	91		693698335	494975421	540414923	654926705	201542	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91351		0.22865		0.77723		0.49805		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24839	24839	SRR25509991	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S67_L002_I1_001.fastq.gz Kristen_10X_101620_S67_L002_R1_001.fastq.gz Kristen_10X_101620_S67_L002_R2_001.fastq.gz	fastq fastq fastq	4430975390.0	34889570.0	GSM7680082 r10	0:8 1:28 2:91	A:923557751;C:658731986;G:718325003;T:874072049;N:264081	8	28	91		923557751	658731986	718325003	874072049	264081	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91797		0.22868		0.77863		0.50737		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24840	24840	SRR25509992	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S67_L003_I1_001.fastq.gz Kristen_10X_101620_S67_L003_R1_001.fastq.gz Kristen_10X_101620_S67_L003_R2_001.fastq.gz	fastq fastq fastq	4429223552.0	34875776.0	GSM7680082 r11	0:8 1:28 2:91	A:923277621;C:658440918;G:718036099;T:873676803;N:264175	8	28	91		923277621	658440918	718036099	873676803	264175	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91753		0.22978		0.77942		0.50977		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24841	24841	SRR25509993	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S67_L004_I1_001.fastq.gz Kristen_10X_101620_S67_L004_R1_001.fastq.gz Kristen_10X_101620_S67_L004_R2_001.fastq.gz	fastq fastq fastq	4549656890.0	35824070.0	GSM7680082 r12	0:8 1:28 2:91	A:950423951;C:673969790;G:734760168;T:900554096;N:282365	8	28	91		950423951	673969790	734760168	900554096	282365	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91687		0.23323		0.77932		0.50984		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24842	24842	SRR25509994	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S68_L001_I1_001.fastq.gz Kristen_10X_101620_S68_L001_R1_001.fastq.gz Kristen_10X_101620_S68_L001_R2_001.fastq.gz	fastq fastq fastq	2696456634.0	21231942.0	GSM7680082 r13	0:8 1:28 2:91	A:562209710;C:401113540;G:437836456;T:530785441;N:161575	8	28	91		562209710	401113540	437836456	530785441	161575	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91384		0.22885		0.77912		0.50672		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24843	24843	SRR25509995	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S68_L002_I1_001.fastq.gz Kristen_10X_101620_S68_L002_R1_001.fastq.gz Kristen_10X_101620_S68_L002_R2_001.fastq.gz	fastq fastq fastq	2735162932.0	21536716.0	GSM7680082 r14	0:8 1:28 2:91	A:570169460;C:406846839;G:443964376;T:538696359;N:164122	8	28	91		570169460	406846839	443964376	538696359	164122	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91691		0.22998		0.77942		0.51035		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24844	24844	SRR25509996	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S68_L003_I1_001.fastq.gz Kristen_10X_101620_S68_L003_R1_001.fastq.gz Kristen_10X_101620_S68_L003_R2_001.fastq.gz	fastq fastq fastq	2739703563.0	21572469.0	GSM7680082 r15	0:8 1:28 2:91	A:571283074;C:407511119;G:444574049;T:539563747;N:162690	8	28	91		571283074	407511119	444574049	539563747	162690	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91526		0.22747		0.7793		0.51387		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24845	24845	SRR25509997	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S68_L004_I1_001.fastq.gz Kristen_10X_101620_S68_L004_R1_001.fastq.gz Kristen_10X_101620_S68_L004_R2_001.fastq.gz	fastq fastq fastq	2828960433.0	22275279.0	GSM7680082 r16	0:8 1:28 2:91	A:591166850;C:419193897;G:457332081;T:559181603;N:175958	8	28	91		591166850	419193897	457332081	559181603	175958	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91651		0.23126		0.77613		0.50223		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24846	24846	SRR25509998	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S65_L002_I1_001.fastq.gz Kristen_10X_101620_S65_L002_R1_001.fastq.gz Kristen_10X_101620_S65_L002_R2_001.fastq.gz	fastq fastq fastq	3374189340.0	26568420.0	GSM7680082 r2	0:8 1:28 2:91	A:703424426;C:501911907;G:547786373;T:664402117;N:201397	8	28	91		703424426	501911907	547786373	664402117	201397	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91522		0.22812		0.77753		0.50208		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24847	24847	SRR25509999	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S65_L003_I1_001.fastq.gz Kristen_10X_101620_S65_L003_R1_001.fastq.gz Kristen_10X_101620_S65_L003_R2_001.fastq.gz	fastq fastq fastq	3383217516.0	26639508.0	GSM7680082 r3	0:8 1:28 2:91	A:705514047;C:503189161;G:549089218;T:666200894;N:201908	8	28	91		705514047	503189161	549089218	666200894	201908	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91535		0.23036		0.78078		0.50202		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24848	24848	SRR25510000	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S65_L004_I1_001.fastq.gz Kristen_10X_101620_S65_L004_R1_001.fastq.gz Kristen_10X_101620_S65_L004_R2_001.fastq.gz	fastq fastq fastq	3493154050.0	27505150.0	GSM7680082 r4	0:8 1:28 2:91	A:729910298;C:517582902;G:564926384;T:690333365;N:215701	8	28	91		729910298	517582902	564926384	690333365	215701	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91569		0.22913		0.77873		0.50186		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24849	24849	SRR25510001	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S66_L001_I1_001.fastq.gz Kristen_10X_101620_S66_L001_R1_001.fastq.gz Kristen_10X_101620_S66_L001_R2_001.fastq.gz	fastq fastq fastq	3237456187.0	25491781.0	GSM7680082 r5	0:8 1:28 2:91	A:674885196;C:481871349;G:525642933;T:637154812;N:197781	8	28	91		674885196	481871349	525642933	637154812	197781	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91378		0.22852		0.77843		0.50985		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24850	24850	SRR25510002	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S66_L002_I1_001.fastq.gz Kristen_10X_101620_S66_L002_R1_001.fastq.gz Kristen_10X_101620_S66_L002_R2_001.fastq.gz	fastq fastq fastq	3287789081.0	25888103.0	GSM7680082 r6	0:8 1:28 2:91	A:685408765;C:489232060;G:533550966;T:647427897;N:197685	8	28	91		685408765	489232060	533550966	647427897	197685	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91484		0.22872		0.78001		0.49909		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24851	24851	SRR25510003	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S66_L003_I1_001.fastq.gz Kristen_10X_101620_S66_L003_R1_001.fastq.gz Kristen_10X_101620_S66_L003_R2_001.fastq.gz	fastq fastq fastq	3298207145.0	25970135.0	GSM7680082 r7	0:8 1:28 2:91	A:687621787;C:490851045;G:535230137;T:649382247;N:197069	8	28	91		687621787	490851045	535230137	649382247	197069	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91559		0.2268		0.77766		0.50935		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24852	24852	SRR25510004	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S66_L004_I1_001.fastq.gz Kristen_10X_101620_S66_L004_R1_001.fastq.gz Kristen_10X_101620_S66_L004_R2_001.fastq.gz	fastq fastq fastq	3377888088.0	26597544.0	GSM7680082 r8	0:8 1:28 2:91	A:705624374;C:500985504;G:546306692;T:667248332;N:211602	8	28	91		705624374	500985504	546306692	667248332	211602	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91679		0.22965		0.77837		0.51495		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
24853	24853	SRR25510005	SRX21240518	SRS18495441	SRP453227	PRJNA1001940	Determinants of Motor Neuron Functional Subtypes Important for Locomotor Speed	GSE240026	Transcriptome Analysis	Locomotion requires precise control of the strength and speed of muscle contraction and is achieved by recruiting functionally distinct subtypes of motor neurons MNs. MNs are essential to movement and differentially susceptible in disease but little is known about how MNs acquire functional subtype specific features during development. Using single cell RNA profiling in embryonic and larval zebrafish we identify novel and conserved molecular signatures for MN functional subtypes and identify genes expressed in both early post mitotic and mature MNs. Assessing MN development in genetic mutants we define a molecular program essential for MN functional subtype specification. Two evolutionarily conserved transcription factors Prdm16 and Mecom are both functional subtype specific determinants integral for fast MN development. Loss of prdm16 or mecom causes fast MNs to develop transcriptional profiles and innervation similar to slow MNs. These results reveal the molecular diversity of vertebrate axial MNs and demonstrate that functional subtypes are specified through intrinsic transcriptional codes. Overall design: Spinal cord MNs of WT prdm16 / and mecom / zebrafish embryos at two developmental timepoints 2dpf and 5dpf were isolated by fluorescence activated cell sorting FACS according to the presence of dsRed and GFP signal then analyzed using scRNAseq.		pubmed:37676768		Spinal cord MNs olig2dsRed 2dpf scRNAseq	GSM7680082		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed 2dpf scRNAseq	The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v5.0.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: build GRCz11 Supplementary files format and content: h5 files	tail		DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics.		tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:2dpf\|cell type:Spinal cord MNs	GSM7680082	GSM7680082: Spinal cord MNs olig2dsRed 2dpf scRNAseq; Danio rerio; RNA Seq	GSM7680082 r1	GSM7680082	1	DsRed positive cells were isolated from 2 dpf or 5 dpf control mecom mutant or prdm16 mutant zebrafish embryos on an Tgolig2:DsRed2 or Tgprdm16::GFP;Tgolig2:DsRed2 background. Trunk and tail tissue were separated from cranial tissue. Tissue was then finely chopped using a razor blade dissociated using papain filtered and resuspended for sorting. Cells were sorted using the Sony SH800 FACS Cell Sorter. GFP DsRed2 and single fluorophore control embryos were also included as controls for the FACS setup. DAPI was used for a live/dead marker. Sorted cells were then counted using a hemocytometer and spun down to resuspend at a higher concentration. Cells were then processed using the standard 10x Genomics and CellRangerv5.0.1 pipeline 89. Raw sequencing reads were mapped to the zebrafish reference genome build GRCz11. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP453227		loader:fastq load.py	Kristen_10X_101620_S67_L001_I1_001.fastq.gz Kristen_10X_101620_S67_L001_R1_001.fastq.gz Kristen_10X_101620_S67_L001_R2_001.fastq.gz	fastq fastq fastq	4346114117.0	34221371.0	GSM7680082 r9	0:8 1:28 2:91	A:905838814;C:646261347;G:704993570;T:856789016;N:262014	8	28	91		905838814	646261347	704993570	856789016	262014	SRX21240518	SRS18495441	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91558		0.22834		0.7783		0.49972		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Hatching	Embryo	Tail	Multi-system
25107	25107	SRR25605432	SRX21332628	SRS18578260	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep3	GSM7702835		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702835	GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq	GSM7702835 r1	GSM7702835	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz	fastq fastq fastq fastq	21603309774.0	156545723.0	GSM7702835 r1	0:10 1:10 2:28 3:90	A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216	10	10	28	90	3960451458	3105338977	3480072824	3541218595	2033216	SRX21332628	SRS18578260	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94286		0.14175		0.78395		0.51541		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25108	25108	SRR25605433	SRX21332628	SRS18578260	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep3	GSM7702835		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702835	GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq	GSM7702835 r1	GSM7702835	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz	fastq fastq fastq fastq	22413465270.0	162416415.0	GSM7702835 r2	0:10 1:10 2:28 3:90	A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021	10	10	28	90	4104405257	3220235633	3625448968	3667329471	58021	SRX21332628	SRS18578260	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94239		0.14234		0.78338		0.50616		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25109	25109	SRR25822232	SRX21332628	SRS18578260	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep3	GSM7702835		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702835	GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq	GSM7702835 r1	GSM7702835	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz	fastq fastq fastq fastq	21424338264.0	155248828.0	GSM7702835 r3	0:10 1:10 2:28 3:90	A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932	10	10	28	90	3928077020	3077672525	3451667186	3513734857	1242932	SRX21332628	SRS18578260	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.9433		0.14242		0.78328		0.52384		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25110	25110	SRR25822233	SRX21332628	SRS18578260	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep3	GSM7702835		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702835	GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq	GSM7702835 r1	GSM7702835	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz	fastq fastq fastq fastq	22542479952.0	163351304.0	GSM7702835 r4	0:10 1:10 2:28 3:90	A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485	10	10	28	90	4130174287	3235362228	3643457599	3691295761	1327485	SRX21332628	SRS18578260	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94183		0.14124		0.78301		0.50517		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25111	25111	SRR25605434	SRX21332627	SRS18578259	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep3	GSM7702834		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702834	GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq	GSM7702834 r1	GSM7702834	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz	fastq fastq fastq fastq	20161522758.0	146097991.0	GSM7702834 r1	0:10 1:10 2:28 3:90	A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112	10	10	28	90	3649819934	2958286158	3267504300	3271384686	1824112	SRX21332627	SRS18578259	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94851		0.1483		0.80012		0.52549		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25112	25112	SRR25605435	SRX21332627	SRS18578259	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep3	GSM7702834		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702834	GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq	GSM7702834 r1	GSM7702834	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz	fastq fastq fastq fastq	20708273928.0	150059956.0	GSM7702834 r2	0:10 1:10 2:28 3:90	A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351	10	10	28	90	3746088654	3037032642	3368938151	3353289242	47351	SRX21332627	SRS18578259	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94778		0.14581		0.80028		0.52885		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25113	25113	SRR25822230	SRX21332627	SRS18578259	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep3	GSM7702834		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702834	GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq	GSM7702834 r1	GSM7702834	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz	fastq fastq fastq fastq	20078121078.0	145493631.0	GSM7702834 r3	0:10 1:10 2:28 3:90	A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962	10	10	28	90	3634984131	2943891505	3255149272	3259243920	1157962	SRX21332627	SRS18578259	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94884		0.14622		0.80099		0.52572		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25114	25114	SRR25822231	SRX21332627	SRS18578259	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep3	GSM7702834		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep3	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702834	GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq	GSM7702834 r1	GSM7702834	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz	fastq fastq fastq fastq	20884392978.0	151336181.0	GSM7702834 r4	0:10 1:10 2:28 3:90	A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970	10	10	28	90	3779370721	3059502508	3396295214	3383865877	1221970	SRX21332627	SRS18578259	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.94896		0.14559		0.8002		0.51418		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25115	25115	SRR25605436	SRX21332626	SRS18578258	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep2	GSM7702833		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702833	GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq	GSM7702833 r1	GSM7702833	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py\|options: allowEarlyFileEnd	1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz	fastq fastq fastq fastq	22174775364.0	160686778.0	GSM7702833 r1	0:10 1:10 2:28 3:90	A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885	10	10	28	90	4207510387	3050740898	3362227609	3839333241	1997885	SRX21332626	SRS18578258	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93287		0.11844		0.81087		0.55264		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25116	25116	SRR25605437	SRX21332626	SRS18578258	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep2	GSM7702833		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702833	GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq	GSM7702833 r1	GSM7702833	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py\|options: allowEarlyFileEnd	1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	22047847518.0	159767011.0	GSM7702833 r2	0:10 1:10 2:28 3:90	A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001	10	10	28	90	4174013532	3033959926	3357962867	3813042664	52001	SRX21332626	SRS18578258	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93359		0.11585		0.81087		0.55705		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25117	25117	SRR25822228	SRX21332626	SRS18578258	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep2	GSM7702833		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702833	GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq	GSM7702833 r1	GSM7702833	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz	fastq fastq fastq fastq	22010894568.0	159499236.0	GSM7702833 r3	0:10 1:10 2:28 3:90	A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918	10	10	28	90	4176090595	3026940106	3336506731	3814128890	1264918	SRX21332626	SRS18578258	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93457		0.11733		0.81032		0.55203		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25118	25118	SRR25822229	SRX21332626	SRS18578258	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep2	GSM7702833		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702833	GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq	GSM7702833 r1	GSM7702833	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz	fastq fastq fastq fastq	22227220746.0	161066817.0	GSM7702833 r4	0:10 1:10 2:28 3:90	A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858	10	10	28	90	4209198596	3055507768	3382717459	3847294849	1294858	SRX21332626	SRS18578258	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93428		0.11629		0.81014		0.56014		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25119	25119	SRR25605438	SRX21332625	SRS18578257	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep2	GSM7702832		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702832	GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq	GSM7702832 r1	GSM7702832	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	25141955454.0	182188083.0	GSM7702832 r1	0:10 1:10 2:28 3:90	A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244	10	10	28	90	4942067104	3446689328	3778138998	4227670796	2361244	SRX21332625	SRS18578257	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.90803		0.11273		0.81872		0.54345		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25120	25120	SRR25605439	SRX21332625	SRS18578257	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep2	GSM7702832		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702832	GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq	GSM7702832 r1	GSM7702832	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz	fastq fastq fastq fastq	25433730786.0	184302397.0	GSM7702832 r2	0:10 1:10 2:28 3:90	A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122	10	10	28	90	4980326106	3488986366	3842594871	4275245265	63122	SRX21332625	SRS18578257	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.91035		0.11175		0.82016		0.52814		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25121	25121	SRR25822226	SRX21332625	SRS18578257	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep2	GSM7702832		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702832	GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq	GSM7702832 r1	GSM7702832	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz	fastq fastq fastq fastq	24834656088.0	179961276.0	GSM7702832 r3	0:10 1:10 2:28 3:90	A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685	10	10	28	90	4878672093	3403443000	3732878174	4180051888	1469685	SRX21332625	SRS18578257	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.90776		0.11325		0.81852		0.54011		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25122	25122	SRR25822227	SRX21332625	SRS18578257	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep2	GSM7702832		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep2	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702832	GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq	GSM7702832 r1	GSM7702832	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz	fastq fastq fastq fastq	25609437216.0	185575632.0	GSM7702832 r4	0:10 1:10 2:28 3:90	A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424	10	10	28	90	5015380345	3509305882	3867598814	4308011415	1510424	SRX21332625	SRS18578257	SRA1702612	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.90907		0.11192		0.81994		0.50902		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25123	25123	SRR25605440	SRX21332624	SRS18578256	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep1	GSM7702831		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep1	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702831	GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq	GSM7702831 r1	GSM7702831	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	gfp_nre_S1_L001_R2_001.fastq.gz gfp_nre_S1_L001_R1_001.fastq.gz gfp_nre_S1_L001_I2_001.fastq.gz gfp_nre_S1_L001_I1_001.fastq.gz	fastq fastq fastq fastq	47873499684.0	346909418.0	GSM7702831 r1	0:10 1:10 2:28 3:90	A:8912593789;C:6786299583;G:7771099171;T:7737013838;N:14841239	10	10	28	90	8912593789	6786299583	7771099171	7737013838	14841239	SRX21332624	SRS18578256	SRA1690580	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.90717		0.15854		0.80501		0.50927		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25124	25124	SRR25605441	SRX21332624	SRS18578256	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		gfp enriched rep1	GSM7702831		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	gfp enriched rep1	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702831	GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq	GSM7702831 r1	GSM7702831	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	gfp_nre_S1_L002_I1_001.fastq.gz gfp_nre_S1_L002_I2_001.fastq.gz gfp_nre_S1_L002_R1_001.fastq.gz gfp_nre_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	48659347860.0	352603970.0	GSM7702831 r2	0:10 1:10 2:28 3:90	A:9056524463;C:6888387179;G:7922807308;T:7854042793;N:12595557	10	10	28	90	9056524463	6888387179	7922807308	7854042793	12595557	SRX21332624	SRS18578256	SRA1690580	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.90541		0.15686		0.80543		0.51051		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25125	25125	SRR25605442	SRX21332623	SRS18578255	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep1	GSM7702830		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep1	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702830	GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq	GSM7702830 r1	GSM7702830	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	double_pos_S2_L001_R2_001.fastq.gz double_pos_S2_L001_R1_001.fastq.gz double_pos_S2_L001_I2_001.fastq.gz double_pos_S2_L001_I1_001.fastq.gz	fastq fastq fastq fastq	41371188084.0	299791218.0	GSM7702830 r1	0:10 1:10 2:28 3:90	A:7690531012;C:5787287634;G:6514950407;T:6975618202;N:12822365	10	10	28	90	7690531012	5787287634	6514950407	6975618202	12822365	SRX21332623	SRS18578255	SRA1690580	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93894		0.17677		0.79926		0.51122		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
25126	25126	SRR25605443	SRX21332623	SRS18578255	SRP454539	PRJNA1004255	Unique activities of two overlapping PAX6 retinal enhancers	GSE240575	Transcriptome Analysis	Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.		pubmed:37643867		mcherry enriched rep1	GSM7702830		source name:Eye\|tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf\|geo loc name:missing\|collection date:missing	mcherry enriched rep1	Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted…	Eye		NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.		tissue:Eye\|genotype:NRE eGFP/HS5 mCherry\|developmental stage:48 hpf	GSM7702830	GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq	GSM7702830 r1	GSM7702830	1	NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP454539		loader:fastq load.py	double_pos_S2_L002_I1_001.fastq.gz double_pos_S2_L002_I2_001.fastq.gz double_pos_S2_L002_R1_001.fastq.gz double_pos_S2_L002_R2_001.fastq.gz	fastq fastq fastq fastq	42692812980.0	309368210.0	GSM7702830 r2	0:10 1:10 2:28 3:90	A:7933061913;C:5964617781;G:6744802923;T:7189579846;N:11076437	10	10	28	90	7933061913	5964617781	6744802923	7189579846	11076437	SRX21332623	SRS18578255	SRA1690580	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh	1	0.93887		0.17578		0.79825		0.50169		90		B		usable mapping rate	illumina	nextseq_v2	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2023-08-10	Hatching	Embryo	Eye	Sensory System
26483	26483	SRR25930975	SRX21649988	SRS18818460	SRP458853	PRJNA1013567	scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts	GSE242483	Transcriptome Analysis	Seeking to identify additional transcription factors required for cardiac valve formation we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established and at 80 hpf when forming valves are first observed		pubmed:38748804		50hpf	GSM7764481		source name:heart\|tissue:heart\|genotype:wild type\|age:50hpf\|geo loc name:missing\|collection date:missing	50hpf	Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs	heart		Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000		tissue:heart\|genotype:wild type\|age:50hpf	GSM7764481	GSM7764481: 50hpf; Danio rerio; RNA Seq	GSM7764481 r1	GSM7764481	1	Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP458853			Giulia_50hpf_S1_R2_001.fastq.gz Giulia_50hpf_S1_R1_001.fastq.gz	fastq fastq	19874763820.0	237988724.0	GSM7764481 r1	0:28 1:55.51	A:5320257914;C:4424267230;G:4320623789;T:5708249185;N:101365702	28	55			5320257914	4424267230	4320623789	5708249185	101365702	SRX21649988	SRS18818460	SRA1706674	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	2	0.00185	0.94414	0.00087	0.13397	0.99675	0.80172	0.41142	0.51985	28	56	T	B	sc-like readlen	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2023-09-06	Hatching	Embryo	Heart	Cardiovascular System
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
32609	32609	SRR29325925	SRX24842084	SRS21553259	SRP512516	PRJNA1121299	Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study "The heart is a niche for hematopoietic stem and progenitor cells in zebrafish."	GSE269378	Transcriptome Analysis	We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study we uncovered the presence of an endocardial hematopoietic cluster along with other significant clusters including valve endocardial and interstitial cells and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells and further analyzed using scRNAseq.		pubmed:39217144		EC 2d	GSM8314110		source name:Heart\|tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:48 hpf loc name:missing\|collection date:missing	EC 2d	Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding McInnes & Healy https://arxiv.org/abs/1802.03426 and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs	Heart		Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Ne…	Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf	tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:48 hpf	GSM8314110	GSM8314110: EC 2d; Danio rerio; RNA Seq	GSM8314110 r1	GSM8314110	1	Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Ne…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP512516			Felix_10x_Lib_EC-2d_R1.fastq.gz Felix_10x_Lib_EC-2d_R2.fastq.gz	fastq fastq	37849382027.0	476135961.0	GSM8314110 r1	0:28 1:51.49	A:10212120425;C:8162504214;G:8573129268;T:10704929378;N:196698742	28	51			10212120425	8162504214	8573129268	10704929378	196698742	SRX24842084	SRS21553259	SRA1892449	MPI for heart and lung research	MPI for heart and lung research												T	B	mate1 technical by mapping diff	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2024-06-07	Hatching	Embryo	Heart	Cardiovascular System
32863	32863	SRR30114185	SRX25586802	SRS22237546	SRP523914	PRJNA1126282	Danio rerio Single cell Transcriptome	PRJNA1126282	Transcriptome Analysis	Single cell sequencing of Zebrafish model with RFC1 mutation for loss of function study. Samples from zebrafishes at 2 or 4 dpf isolated from the whole head or whole brain respectively. Libraries prepared and sequenced with 10X Genomics three prime Chromium kits.				WT sc 2dpf	WT sc 2dpf S1 L003		strain:Tgrfc1+/+\|age:2dpf\|collection date:2024 02 19\|geo loc name:Canada: Montreal\|sex:N/A\|tissue:Head\|genotype:Wild Type\|BioSampleModel:Model organism or animal									scRNA Seq of danio rerio: 2dpf head	WT sc 2dpf	WT sc 2dpf	Four brains or three heads per condition from 4dpf or 2dpf larvae respectively were transferred into 1.5ml tubes containing 250 l of papain solution 100l papain 100l DNase I and 200l L cysteine per 5 mL of DMEM/F12. The tissue was digested 20min at 37C with pipetting every 10min. Enzymatic digestion was stopped with washing solution 65l glucose 45 % 50L HEPES 1M and 0.5ml FBS qsp 10ml DPBS 1X and centrifuged at 800g for 5min at 4C. Supernatant was removed and pellet was resuspended in 50l of washing solution. The cell suspension was filtered with a cell strainer to remove aggregates. Libraries were prepared with a three prime Chromium kit and sent for 10X Genomics sequencing at a depth of 250 million reads 100bp ea from Illumina NovaSeq6000.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP523914			WT_sc_2dpf_S1_L003_R2.fastq.gz WT_sc_2dpf_S1_L003_R1.fastq.gz	fastq fastq	56807165786.0	281223593.0	WT sc 2dpf S1 L003 R1.fastq.gz	0:101 1:101	A:15279867415;C:9333139424;G:10011041111;T:22182483036;N:634800	101	101			15279867415	9333139424	10011041111	22182483036	634800	SRX25586802	SRS22237546	SRA1936077	CHUM Research Center\|Neurosciences	CHUM Research Center	2	0.07599	0.93395	0.0191	0.17781	0.97636	0.81215	0.61682	0.56234	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2024-08-02	Hatching	Embryo	Head	Nervous System
32864	32864	SRR30114186	SRX25586801	SRS22237545	SRP523914	PRJNA1126282	Danio rerio Single cell Transcriptome	PRJNA1126282	Transcriptome Analysis	Single cell sequencing of Zebrafish model with RFC1 mutation for loss of function study. Samples from zebrafishes at 2 or 4 dpf isolated from the whole head or whole brain respectively. Libraries prepared and sequenced with 10X Genomics three prime Chromium kits.				RFC1 KO sc 2dpf	RFC1 KO sc 2dpf S2 L003		strain:Tgrfc1 / \|age:2dpf\|collection date:2024 02 19\|geo loc name:Canada: Montreal\|sex:N/A\|tissue:Head\|genotype:RFC1 KO\|BioSampleModel:Model organism or animal									scRNA Seq of danio rerio: 2dpf head	RFC1 KO sc 2dpf	RFC1 KO sc 2dpf	Four brains or three heads per condition from 4dpf or 2dpf larvae respectively were transferred into 1.5ml tubes containing 250 l of papain solution 100l papain 100l DNase I and 200l L cysteine per 5 mL of DMEM/F12. The tissue was digested 20min at 37C with pipetting every 10min. Enzymatic digestion was stopped with washing solution 65l glucose 45 % 50L HEPES 1M and 0.5ml FBS qsp 10ml DPBS 1X and centrifuged at 800g for 5min at 4C. Supernatant was removed and pellet was resuspended in 50l of washing solution. The cell suspension was filtered with a cell strainer to remove aggregates. Libraries were prepared with a three prime Chromium kit and sent for 10X Genomics sequencing at a depth of 250 million reads 100bp ea from Illumina NovaSeq6000.			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP523914			RFC1-KO_sc_2dpf_S2_L003_R1.fastq.gz RFC1-KO_sc_2dpf_S2_L003_R2.fastq.gz	fastq fastq	45448109280.0	224990640.0	RFC1 KO sc 2dpf S2 L003 R1.fastq.gz	0:101 1:101	A:12090767157;C:7635667126;G:8209912637;T:17511260653;N:501707	101	101			12090767157	7635667126	8209912637	17511260653	501707	SRX25586801	SRS22237545	SRA1936077	CHUM Research Center\|Neurosciences	CHUM Research Center	2	0.09244	0.93268	0.02271	0.19887	0.97544	0.80955	0.6375	0.56143	101	101	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Canada	2024-08-02	Hatching	Embryo	Head	Nervous System
33425	33425	SRR30186680	SRX25652375	SRS22295177	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS2dpf	GSM8448582		source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf\|geo loc name:missing\|collection date:missing	ENS2dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf	GSM8448582	GSM8448582: ENS2dpf; Danio rerio; RNA Seq	GSM8448582 r1	GSM8448582	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP525362		loader:fastq load.py	FT-SA26633_S1_L005_I1_001.fastq.gz FT-SA26633_S1_L005_R1_001.fastq.gz FT-SA26633_S1_L005_R2_001.fastq.gz	fastq fastq fastq	16641390240.0	53681904.0	GSM8448582 r1	0:8 1:151 2:151	A:3957785280;C:2573469243;G:2993166279;T:6685407270;N:2106936	8	151	151		3957785280	2573469243	2993166279	6685407270	2106936	SRX25652375	SRS22295177	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Hatching	Embryo	Gut	Digestive System
33426	33426	SRR30186681	SRX25652375	SRS22295177	SRP525362	PRJNA1146366	Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level	GSE274407	Transcriptome Analysis	Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.		pubmed:39642879		ENS2dpf	GSM8448582		source name:intestine\|tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf\|geo loc name:missing\|collection date:missing	ENS2dpf	The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files	intestine		To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		tissue:intestine\|cell type:Cells in the ENS\|genotype:Phox2bb:mNeonGreen heterozygous\|age:2dpf	GSM8448582	GSM8448582: ENS2dpf; Danio rerio; RNA Seq	GSM8448582 r1	GSM8448582	1	To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP525362		loader:fastq load.py	FT-SA26633_S1_L006_I1_001.fastq.gz FT-SA26633_S1_L006_R1_001.fastq.gz FT-SA26633_S1_L006_R2_001.fastq.gz	fastq fastq fastq	17304656010.0	55821471.0	GSM8448582 r2	0:8 1:151 2:151	A:4101777717;C:2763806899;G:3078134302;T:6911601509;N:2763815	8	151	151		4101777717	2763806899	3078134302	6911601509	2763815	SRX25652375	SRS22295177	SRA1943746	Bronner lab, Biology and Biological Engineering, Caltech	Bronner lab, Biology and Biological Engineering, Caltech												T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2024-08-09	Hatching	Embryo	Gut	Digestive System
35385	35385	SRR32649448	SRX27953870	SRS24319775	SRP569567	PRJNA1234533	Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb	GSE291626	Transcriptome Analysis	To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.				OMP positive Olfactory Sensory Neurons from 48pf Zebrafish	GSM8838717		source name:Olfactory Sensory Tissue\|tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:48 hpf\|genotype:Tgomp:lyn RFP\|geo loc name:missing\|collection date:missing	OMP positive Olfactory Sensory Neurons from 48pf Zebrafish	Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.	Olfactory Sensory Tissue		10X Genomics V3.3		tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:48 hpf\|genotype:Tgomp:lyn RFP	GSM8838717	GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq	GSM8838717 r1	GSM8838717	1	10X Genomics V3.3		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP569567		loader:fastq load.py	97364_S5_L001_I1_001.fastq.gz 97364_S5_L001_R1_001.fastq.gz 97364_S5_L001_R2_001.fastq.gz	fastq fastq fastq	7455743360.0	57351872.0	GSM8838717 r1	0:8 1:28 2:94	A:1588619193;C:1118423731;G:1232237797;T:1451670240;N:125007	8	28	94		1588619193	1118423731	1232237797	1451670240	125007	SRX27953870	SRS24319775	SRA2091725	Department of Neuroscience, University of Pennsylvania	Department of Neuroscience, University of Pennsylvania												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-11	Hatching	Embryo	Brain	Nervous System
35386	35386	SRR32649449	SRX27953870	SRS24319775	SRP569567	PRJNA1234533	Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb	GSE291626	Transcriptome Analysis	To understand how neural circuits are assembled it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family pcdh7b and pcdh11 are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast two members of the delta2 protocadherin family pcdh10b and pcdh17 are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36 48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.				OMP positive Olfactory Sensory Neurons from 48pf Zebrafish	GSM8838717		source name:Olfactory Sensory Tissue\|tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:48 hpf\|genotype:Tgomp:lyn RFP\|geo loc name:missing\|collection date:missing	OMP positive Olfactory Sensory Neurons from 48pf Zebrafish	Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.	Olfactory Sensory Tissue		10X Genomics V3.3		tissue:Olfactory Sensory Tissue\|cell line:Olactory Sensory Neurons\|cell type:Neurons\|sample age:48 hpf\|genotype:Tgomp:lyn RFP	GSM8838717	GSM8838717: OMP positive Olfactory Sensory Neurons from 48pf Zebrafish; Danio rerio; RNA Seq	GSM8838717 r1	GSM8838717	1	10X Genomics V3.3		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP569567		loader:fastq load.py	97364_S5_L002_I1_001.fastq.gz 97364_S5_L002_R1_001.fastq.gz 97364_S5_L002_R2_001.fastq.gz	fastq fastq fastq	7445521460.0	57273242.0	GSM8838717 r2	0:8 1:28 2:94	A:1586585615;C:1115323543;G:1231863598;T:1449738354;N:173638	8	28	94		1586585615	1115323543	1231863598	1449738354	173638	SRX27953870	SRS24319775	SRA2091725	Department of Neuroscience, University of Pennsylvania	Department of Neuroscience, University of Pennsylvania												B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2025-03-11	Hatching	Embryo	Brain	Nervous System
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
50656	50656	SRR10769144	SRX7443062	SRS5887360	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		48 hpf retina rep	GSM4233148		source name:Retina\|strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:48 hpf	48 hpf 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 subtract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples we subtract 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:whole retina\|developmental stage:48 hpf	GSM4233148	GSM4233148: 48 hpf retina rep; Danio rerio; RNA Seq	GSM4233148		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:GSM4233148	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565		intentional duplicate	48hpf_rep_possorted_genome_bam.bam	10X Genomics bam file	31477860150.0	209852401.0	GSM4233148 r1	0:150	A:9531250692;C:6384514147;G:7053602060;T:8508157890;N:335361	150				9531250692	6384514147	7053602060	8508157890	335361	SRX7443062	SRS5887360	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.91107		0.07208		0.83644		0.47681		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2019-12-26	Hatching	Embryo	Eye	Sensory System
50661	50661	SRR11812054	SRX5025779	SRS4057279	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		48 hpf retina	GSM3478015		source name:Retina\|strain:AB\|genotype:wildtype\|tissue:whole retina\|developmental stage:48 hpf	48 hpf 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:whole retina\|developmental stage:48 hpf	GSM3478015	GSM3478015: 48 hpf retina; Danio rerio; RNA Seq	GSM3478015		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:GSM3478015	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP169565		intentional duplicate	48hpf_possorted_genome_bam.bam	10X Genomics bam file	27828827400.0	185525516.0	GSM3478015 r11	0:150	A:8568529313;C:5431445717;G:5968188905;T:7860573445;N:90020	150				8568529313	5431445717	5968188905	7860573445	90020	SRX5025779	SRS4057279	SRA812747	GEO	Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS	1	0.91308		0.11004		0.82213		0.48772		150		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2018-11-19	Hatching	Embryo	Eye	Sensory System
54190	54190	SRR10095966	SRX6828143	SRS5370318	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					2b		strain:Tgolig2:GFPvu12\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2b\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	2b	2b	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273		loader:latf load	olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	100194025377.0	630151103.0	2b.gz	0:26 1:133	A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462	26	133			27235389395	22388810842	23041272930	27513445748	15106462	SRX6828143	SRS5370318	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.0127	0.95456	0.00215	0.09469	0.97463	0.79308	0.43287	0.50046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
54191	54191	SRR10095967	SRX6828142	SRS5370317	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					2a		strain:Tgelavl3:GCaMP6s\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2a\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	2a	2a	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	NextSeq 500	SRP221273		loader:latf load	2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq	30654488793.0	192795527.0	2a.gz	0:26 1:133	A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245	26	133			8922702024	6370087682	7321183700	8019014142	21501245	SRX6828142	SRS5370317	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.00427	0.91705	0.00106	0.08701	0.98999	0.8198	0.35255	0.50555	26	133	T	B	sc-like readlen	illumina	nextseq	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
59879	59879	SRR12060553	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 68 70hpf	GSM4629199		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L001 R1 001.fastq read2PairFiles=GFPplus S1 L001 R2 001.fastq read3PairFiles=GFPplus S1 L001 I1 001.fastq	GFPplus_S1_L001_I1_001.fastq GFPplus_S1_L001_R1_001.fastq GFPplus_S1_L001_R2_001.fastq	fastq fastq fastq	6274319830.0	39710885.0	GSM4629199 r1	0:26 1:124 2:8	A:1841798453;C:1283501945;G:1425301974;T:1723079104;N:638354	26	124	8		1841798453	1283501945	1425301974	1723079104	638354	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00247	0.91739	0.00057	0.08148	0.99486	0.8098	0.40168	0.49704	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59880	59880	SRR12060554	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 68 70hpf	GSM4629199		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L002 R1 001.fastq read2PairFiles=GFPplus S1 L002 R2 001.fastq read3PairFiles=GFPplus S1 L002 I1 001.fastq			3615497884.0	22882898.0	GSM4629199 r2	0:26 1:124 2:8	A:1062722875;C:724671651;G:825496420;T:1002262450;N:344488	26	124	8		1062722875	724671651	825496420	1002262450	344488	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00228	0.91709	0.00071	0.08087	0.99557	0.80984	0.37288	0.50652	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59881	59881	SRR12060555	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 68 70hpf	GSM4629199		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L003 R1 001.fastq read2PairFiles=GFPplus S1 L003 R2 001.fastq read3PairFiles=GFPplus S1 L003 I1 001.fastq	GFPplus_S1_L003_I1_001.fastq GFPplus_S1_L003_R1_001.fastq GFPplus_S1_L003_R2_001.fastq	fastq fastq fastq	6350185110.0	40191045.0	GSM4629199 r3	0:26 1:124 2:8	A:1852452135;C:1299393173;G:1456328475;T:1740481266;N:1530061	26	124	8		1852452135	1299393173	1456328475	1740481266	1530061	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00235	0.91442	0.00069	0.08011	0.99535	0.80813	0.37864	0.50714	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59882	59882	SRR12060556	SRX8588729	SRS6880197	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 68 70hpf	GSM4629199		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 68 70hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:68 hpf 70 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629199	GSM4629199: Sox10+ 68 70hpf; Danio rerio; RNA Seq	GSM4629199		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629199	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: allowEarlyFileEnd platform=Illumina readTypes=BBT read1PairFiles=GFPplus S1 L004 R1 001.fastq read2PairFiles=GFPplus S1 L004 R2 001.fastq read3PairFiles=GFPplus S1 L004 I1 001.fastq			5812557404.0	36788338.0	GSM4629199 r4	0:26 1:124 2:8	A:1702052926;C:1187088636;G:1324270973;T:1598146532;N:998337	26	124	8		1702052926	1187088636	1324270973	1598146532	998337	SRX8588729	SRS6880197	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.00277	0.91719	0.00069	0.08091	0.9945	0.80783	0.39641	0.51387	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59883	59883	SRR12060549	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 48 50hpf	GSM4629198		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L001 R1 001 mod.fastq read2PairFiles=Sox10Enriched 48h S1 L001 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L001 I1 001 mod.fastq			1616949090.0	10233855.0	GSM4629198 r1	0:26 1:124 2:8	A:456678394;C:358389976;G:376486936;T:425174329;N:219455	26	124	8		456678394	358389976	376486936	425174329	219455	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01006	0.95005	0.00118	0.07248	0.98175	0.8351	0.41141	0.49367	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59884	59884	SRR12060550	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 48 50hpf	GSM4629198		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L002 R1 001 mod.fastq read2PairFiles=Sox10Enriched 48h S1 L002 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L002 I1 001 mod.fastq			1382737000.0	8751500.0	GSM4629198 r2	0:26 1:124 2:8	A:393565729;C:306444540;G:319283385;T:363276484;N:166862	26	124	8		393565729	306444540	319283385	363276484	166862	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01049	0.94963	0.00135	0.07338	0.98192	0.83952	0.3958	0.49146	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59885	59885	SRR12060551	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 48 50hpf	GSM4629198		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L003 R1 001.fastq read2PairFiles=Sox10Enriched 48h S1 L003 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L003 I1 001.fastq	Sox10Enriched_48h_S1_L003_I1_001.fastq Sox10Enriched_48h_S1_L003_R1_001.fastq Sox10Enriched_48h_S1_L003_R2_001.fastq	fastq fastq fastq	7027816932.0	44479854.0	GSM4629198 r3	0:26 1:124 2:8	A:1977891064;C:1517642706;G:1691754065;T:1838521085;N:2008012	26	124	8		1977891064	1517642706	1691754065	1838521085	2008012	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01071	0.94964	0.00138	0.06976	0.98123	0.83116	0.39988	0.4831	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
59886	59886	SRR12060552	SRX8588728	SRS6880196	SRP268145	PRJNA640816	An atlas of neural crest lineages along the posterior developing zebrafish at single cell resolution	GSE152906	Transcriptome Analysis	Neural crest cells NCCs are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here we utilized single cell transcriptomic analyses to delineate NCC derivatives along the posterior developing vertebrate zebrafish during the late embryonic to early larval stage a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC derived cell types including mesenchyme neural crest neural neuronal glial and pigment from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages mesenchyme subtypes and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes with distinct profiles within neuronal cells. From these analyses we present a comprehensive cell type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation. Overall design: To characterize the neural crest cell lineages present in the posterior zebrafish during the embryonic to larval transition 48 hpf 72 hpf we utilized single cell RNA sequencing scRNA Seq on the 10x Genomics Chromium platform to build a dataset from GFP+ cells collected from sox10:GFP embryos.		pubmed:33591267;pubmed:38234831;pubmed:38809858		Sox10+ 48 50hpf	GSM4629198		tissue:Derivative Sox10+ Neural Crest\|genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	Sox10+ 48 50hpf	Illumina NextSeq 500 used for basecalling CellRanger v2.1.0 software facilitated genomic alignment filtering barcode reading and exportation for further analysis Genome build: DanioGRCz10 Supplementary files format and content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes barcodes.tsv and genes genes.tsv; 10X Genomics Chromium Raw Gene BC Cellular Matrix matrix.mtx	Derivative Sox10+ Neural Crest	none	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	Embryos were collected synchronously batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1 phenyl 2 thiourea PTU/E3 solution. At 24 hpf embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with Rice University Institutional Animal Care and Use Committee IACUC.	genotype/variation: 4.9sox10:EGFP ba2Tg\|developmental stage:48 hpf 50 hpf\|cell type:FACS isolated 4.9sox10:EGFP+ cells	GSM4629198	GSM4629198: Sox10+ 48 50hpf; Danio rerio; RNA Seq	GSM4629198		1	Posterior tissue Vagal and trunk domains were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer Sigma Aldrich A7089 for 30 45 minutes. Suspension was washed in Hank's Buffer 1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES concentrated via centrifugation 200 rcf for 10 minutes at 4°C in a small volume of Hank's buffer and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell three prime V2 chemistry kit for 10 000 cells. RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline	GEO Accession:GSM4629198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP268145		loader:fastq load.py\|options: platform=Illumina readTypes=BBT read1PairFiles=Sox10Enriched 48h S1 L004 R1 001.fastq read2PairFiles=Sox10Enriched 48h S1 L004 R2 001.fastq read3PairFiles=Sox10Enriched 48h S1 L004 I1 001.fastq			6734234423.0	42621737.0	GSM4629198 r4	0:26 1:124.00 2:8	A:1913564054;C:1452205902;G:1601358930;T:1764533329;N:2572208	26	124	8		1913564054	1452205902	1601358930	1764533329	2572208	SRX8588728	SRS6880196	SRA1089349	GEO	The Uribe Laboratory, BioSciences, Rice University	2	0.01026	0.95184	0.00128	0.07207	0.98244	0.835	0.40661	0.49631	26	124	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-06-20	Hatching	Embryo	Brain	Nervous System
60587	60587	SRR12424278	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_1_S41_L001_R1_001.fastq.gz olig2_egfp_48hpf_1_S41_L001_R2_001.fastq.gz	fastq fastq	18778651430.0	62180965.0	GSM4718658 r1	0:151 1:151	A:6542554044;C:3515052559;G:3489753648;T:5231107020;N:184159	151	151			6542554044	3515052559	3489753648	5231107020	184159	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90055	0.0	0.21162	1.0	0.77776		0.53718	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60588	60588	SRR12424279	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_2_S42_L001_R1_001.fastq.gz olig2_egfp_48hpf_2_S42_L001_R2_001.fastq.gz	fastq fastq	22242782898.0	73651599.0	GSM4718658 r2	0:151 1:151	A:7753674261;C:4160150132;G:4127581173;T:6201157562;N:219770	151	151			7753674261	4160150132	4127581173	6201157562	219770	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90097	0.0	0.2127	1.0	0.77966		0.54192	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60589	60589	SRR12424280	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_3_S43_L001_R2_001.fastq.gz olig2_egfp_48hpf_3_S43_L001_R1_001.fastq.gz	fastq fastq	25591190986.0	84739043.0	GSM4718658 r3	0:151 1:151	A:8917343424;C:4797392797;G:4757647263;T:7118554564;N:252938	151	151			8917343424	4797392797	4757647263	7118554564	252938	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90089	0.0	0.2095	1.0	0.78078		0.53755	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60590	60590	SRR12424281	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_4_S44_L001_R1_001.fastq.gz olig2_egfp_48hpf_4_S44_L001_R2_001.fastq.gz	fastq fastq	25546281170.0	84590335.0	GSM4718658 r4	0:151 1:151	A:8905009196;C:4774524700;G:4734395060;T:7132103501;N:248713	151	151			8905009196	4774524700	4734395060	7132103501	248713	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90169	0.0	0.21158	1.0	0.77697		0.54006	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60929	60929	SRR12658666	SRX9139724	SRS7381390	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681		cd41:GFPlow runx1 / 2.5dpf	GSM4792209		tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow runx1 / 2.5dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:runx1 / del8 hg96 tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	GSM4792209	GSM4792209: cd41:GFPlow runx1 / 2.5dpf; Danio rerio; RNA Seq	GSM4792209		1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792209	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672		loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC2.A8 runx1 nulls.1.R1.fastq.gz read2PairFiles=SC2.A8 runx1 nulls.1.R2.fastq.gz read3PairFiles=SC2.A8 runx1 nulls.1.I1.fastq.gz	SC2.A8-runx1_nulls.1.I1.fastq.gz SC2.A8-runx1_nulls.1.R1.fastq.gz SC2.A8-runx1_nulls.1.R2.fastq.gz	fastq fastq fastq	38938658748.0	294989839.0	GSM4792209 r1	0:26 1:98 2:8	A:10648313958;C:9159222906;G:9191746077;T:9913634426;N:25741381	26	98	8		10648313958	9159222906	9191746077	9913634426	25741381	SRX9139724	SRS7381390	SRA1126726	GEO	NHGRI	1	0.93897		0.09737		0.87271		0.49815		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Hatching	Embryo	Undetermined	Embryo Imprecise
60930	60930	SRR12658665	SRX9139723	SRS7381389	SRP282672	PRJNA663960	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158099	Transcriptome Analysis	We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf.	parent bioproject:PRJNA663961	pubmed:34492681		cd41:GFPlow WT 2.5dpf	GSM4792208		tissue:sorted cd41:GFPlow\|strain:EK\|genotype/variation:WT tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	cd41:GFPlow WT 2.5dpf	Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx	sorted cd41:GFPlow		Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.		strain:EK\|genotype/variation:WT tgcd41:GFP\|age:2.5 dpf\|cell subset:sorted cd41:GFPlow	GSM4792208	GSM4792208: cd41:GFPlow WT 2.5dpf; Danio rerio; RNA Seq	GSM4792208		1	Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol.	GEO Accession:GSM4792208	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP282672		loader:fastq load.py\|options: platform=Illumina readTypes=TBT read1PairFiles=SC1.A7 WT.1.R1.fastq.gz read2PairFiles=SC1.A7 WT.1.R2.fastq.gz read3PairFiles=SC1.A7 WT.1.I1.fastq.gz	SC1.A7-WT.1.I1.fastq.gz SC1.A7-WT.1.R1.fastq.gz SC1.A7-WT.1.R2.fastq.gz	fastq fastq fastq	32778402756.0	248321233.0	GSM4792208 r1	0:26 1:98 2:8	A:9066035393;C:7671732666;G:7865454744;T:8153280795;N:21899158	26	98	8		9066035393	7671732666	7865454744	8153280795	21899158	SRX9139723	SRS7381389	SRA1126726	GEO	NHGRI	1	0.95064		0.07069		0.86634		0.53298		98		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-16	Hatching	Embryo	Undetermined	Embryo Imprecise
61241	61241	SRR12661744	SRX9142589	SRS7383893	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf6 S4	GSM4793206		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf6 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793206	GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq	GSM4793206		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf6 S4 L001 I1 001.fastq.gz read2PairFiles=zBr2dpf6 S4 L001 R1 001.fastq.gz read3PairFiles=zBr2dpf6 S4 L001 R2 001.fastq.gz	zBr2dpf6_S4_L001_I1_001.fastq.gz zBr2dpf6_S4_L001_R1_001.fastq.gz zBr2dpf6_S4_L001_R2_001.fastq.gz	fastq fastq fastq	1641453328.0	17841884.0	GSM4793206 r1	0:8 1:26 2:58	A:432584064;C:365889139;G:409749859;T:432982043;N:248223	8	26	58		432584064	365889139	409749859	432982043	248223	SRX9142589	SRS7383893	SRA1127180	GEO	Harvard University	1	0.93894		0.10335		0.8141		0.49836		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61242	61242	SRR12661745	SRX9142589	SRS7383893	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf6 S4	GSM4793206		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf6 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793206	GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq	GSM4793206		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf6 S4 L002 I1 001.fastq.gz read2PairFiles=zBr2dpf6 S4 L002 R1 001.fastq.gz read3PairFiles=zBr2dpf6 S4 L002 R2 001.fastq.gz	zBr2dpf6_S4_L002_I1_001.fastq.gz zBr2dpf6_S4_L002_R1_001.fastq.gz zBr2dpf6_S4_L002_R2_001.fastq.gz	fastq fastq fastq	1621686024.0	17627022.0	GSM4793206 r2	0:8 1:26 2:58	A:429417081;C:361894200;G:402117760;T:428002033;N:254950	8	26	58		429417081	361894200	402117760	428002033	254950	SRX9142589	SRS7383893	SRA1127180	GEO	Harvard University	1	0.94217		0.10443		0.81397		0.50325		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61243	61243	SRR12661746	SRX9142589	SRS7383893	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf6 S4	GSM4793206		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf6 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793206	GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq	GSM4793206		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf6 S4 L003 I1 001.fastq.gz read2PairFiles=zBr2dpf6 S4 L003 R1 001.fastq.gz read3PairFiles=zBr2dpf6 S4 L003 R2 001.fastq.gz	zBr2dpf6_S4_L003_I1_001.fastq.gz zBr2dpf6_S4_L003_R1_001.fastq.gz zBr2dpf6_S4_L003_R2_001.fastq.gz	fastq fastq fastq	1609851604.0	17498387.0	GSM4793206 r3	0:8 1:26 2:58	A:426272754;C:358330950;G:399431249;T:425557524;N:259127	8	26	58		426272754	358330950	399431249	425557524	259127	SRX9142589	SRS7383893	SRA1127180	GEO	Harvard University	1	0.94019		0.10522		0.81712		0.51174		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61244	61244	SRR12661747	SRX9142589	SRS7383893	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf6 S4	GSM4793206		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf6 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793206	GSM4793206: zBr2dpf6 S4; Danio rerio; RNA Seq	GSM4793206		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf6 S4 L004 I1 001.fastq.gz read2PairFiles=zBr2dpf6 S4 L004 R1 001.fastq.gz read3PairFiles=zBr2dpf6 S4 L004 R2 001.fastq.gz	zBr2dpf6_S4_L004_I1_001.fastq.gz zBr2dpf6_S4_L004_R1_001.fastq.gz zBr2dpf6_S4_L004_R2_001.fastq.gz	fastq fastq fastq	1585670784.0	17235552.0	GSM4793206 r4	0:8 1:26 2:58	A:420707168;C:353519513;G:392246891;T:418960239;N:236973	8	26	58		420707168	353519513	392246891	418960239	236973	SRX9142589	SRS7383893	SRA1127180	GEO	Harvard University	1	0.94124		0.10456		0.81424		0.49886		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61245	61245	SRR12661740	SRX9142588	SRS7383892	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf5 S3	GSM4793205		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf5 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793205	GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq	GSM4793205		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793205	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf5 S3 L001 I1 001.fastq.gz read2PairFiles=zBr2dpf5 S3 L001 R1 001.fastq.gz read3PairFiles=zBr2dpf5 S3 L001 R2 001.fastq.gz	zBr2dpf5_S3_L001_I1_001.fastq.gz zBr2dpf5_S3_L001_R1_001.fastq.gz zBr2dpf5_S3_L001_R2_001.fastq.gz	fastq fastq fastq	1420148340.0	15436395.0	GSM4793205 r1	0:8 1:26 2:58	A:375964274;C:313803783;G:358392750;T:371775975;N:211558	8	26	58		375964274	313803783	358392750	371775975	211558	SRX9142588	SRS7383892	SRA1127180	GEO	Harvard University	1	0.93862		0.10359		0.81308		0.49243		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61246	61246	SRR12661741	SRX9142588	SRS7383892	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf5 S3	GSM4793205		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf5 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793205	GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq	GSM4793205		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793205	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf5 S3 L002 I1 001.fastq.gz read2PairFiles=zBr2dpf5 S3 L002 R1 001.fastq.gz read3PairFiles=zBr2dpf5 S3 L002 R2 001.fastq.gz	zBr2dpf5_S3_L002_I1_001.fastq.gz zBr2dpf5_S3_L002_R1_001.fastq.gz zBr2dpf5_S3_L002_R2_001.fastq.gz	fastq fastq fastq	1402315152.0	15242556.0	GSM4793205 r2	0:8 1:26 2:58	A:373114373;C:310158948;G:351441489;T:367374392;N:225950	8	26	58		373114373	310158948	351441489	367374392	225950	SRX9142588	SRS7383892	SRA1127180	GEO	Harvard University	1	0.9401		0.10484		0.81635		0.51232		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61247	61247	SRR12661742	SRX9142588	SRS7383892	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf5 S3	GSM4793205		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf5 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793205	GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq	GSM4793205		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793205	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf5 S3 L003 I1 001.fastq.gz read2PairFiles=zBr2dpf5 S3 L003 R1 001.fastq.gz read3PairFiles=zBr2dpf5 S3 L003 R2 001.fastq.gz	zBr2dpf5_S3_L003_I1_001.fastq.gz zBr2dpf5_S3_L003_R1_001.fastq.gz zBr2dpf5_S3_L003_R2_001.fastq.gz	fastq fastq fastq	1390355152.0	15112556.0	GSM4793205 r3	0:8 1:26 2:58	A:369922218;C:306670829;G:348674068;T:364863677;N:224360	8	26	58		369922218	306670829	348674068	364863677	224360	SRX9142588	SRS7383892	SRA1127180	GEO	Harvard University	1	0.93976		0.10547		0.81665		0.49079		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61248	61248	SRR12661743	SRX9142588	SRS7383892	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf5 S3	GSM4793205		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf5 S3	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793205	GSM4793205: zBr2dpf5 S3; Danio rerio; RNA Seq	GSM4793205		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793205	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf5 S3 L004 I1 001.fastq.gz read2PairFiles=zBr2dpf5 S3 L004 R1 001.fastq.gz read3PairFiles=zBr2dpf5 S3 L004 R2 001.fastq.gz	zBr2dpf5_S3_L004_I1_001.fastq.gz zBr2dpf5_S3_L004_R1_001.fastq.gz zBr2dpf5_S3_L004_R2_001.fastq.gz	fastq fastq fastq	1369540980.0	14886315.0	GSM4793205 r4	0:8 1:26 2:58	A:365092529;C:302585103;G:342423761;T:359236028;N:203559	8	26	58		365092529	302585103	342423761	359236028	203559	SRX9142588	SRS7383892	SRA1127180	GEO	Harvard University	1	0.94114		0.1047		0.81874		0.4829		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61249	61249	SRR12661736	SRX9142587	SRS7383891	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf4 S2	GSM4793204		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf4 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793204	GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq	GSM4793204		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793204	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf4 S2 L001 I1 001.fastq.gz read2PairFiles=zBr2dpf4 S2 L001 R1 001.fastq.gz read3PairFiles=zBr2dpf4 S2 L001 R2 001.fastq.gz	zBr2dpf4_S2_L001_I1_001.fastq.gz zBr2dpf4_S2_L001_R1_001.fastq.gz zBr2dpf4_S2_L001_R2_001.fastq.gz	fastq fastq fastq	1239134292.0	13468851.0	GSM4793204 r1	0:8 1:26 2:58	A:328796587;C:274709455;G:312200824;T:323245450;N:181976	8	26	58		328796587	274709455	312200824	323245450	181976	SRX9142587	SRS7383891	SRA1127180	GEO	Harvard University	1	0.93935		0.10222		0.81314		0.49726		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61250	61250	SRR12661737	SRX9142587	SRS7383891	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf4 S2	GSM4793204		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf4 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793204	GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq	GSM4793204		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793204	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf4 S2 L002 I1 001.fastq.gz read2PairFiles=zBr2dpf4 S2 L002 R1 001.fastq.gz read3PairFiles=zBr2dpf4 S2 L002 R2 001.fastq.gz	zBr2dpf4_S2_L002_I1_001.fastq.gz zBr2dpf4_S2_L002_R1_001.fastq.gz zBr2dpf4_S2_L002_R2_001.fastq.gz	fastq fastq fastq	1223186368.0	13295504.0	GSM4793204 r2	0:8 1:26 2:58	A:326139052;C:271416638;G:306130792;T:319309928;N:189958	8	26	58		326139052	271416638	306130792	319309928	189958	SRX9142587	SRS7383891	SRA1127180	GEO	Harvard University	1	0.94151		0.10408		0.8155		0.49165		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61251	61251	SRR12661738	SRX9142587	SRS7383891	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf4 S2	GSM4793204		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf4 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793204	GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq	GSM4793204		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793204	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf4 S2 L003 I1 001.fastq.gz read2PairFiles=zBr2dpf4 S2 L003 R1 001.fastq.gz read3PairFiles=zBr2dpf4 S2 L003 R2 001.fastq.gz	zBr2dpf4_S2_L003_I1_001.fastq.gz zBr2dpf4_S2_L003_R1_001.fastq.gz zBr2dpf4_S2_L003_R2_001.fastq.gz	fastq fastq fastq	1202575884.0	13071477.0	GSM4793204 r3	0:8 1:26 2:58	A:320734552;C:265990332;G:301153552;T:314497332;N:200116	8	26	58		320734552	265990332	301153552	314497332	200116	SRX9142587	SRS7383891	SRA1127180	GEO	Harvard University	1	0.9402		0.10292		0.82063		0.47643		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61252	61252	SRR12661739	SRX9142587	SRS7383891	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf4 S2	GSM4793204		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf4 S2	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793204	GSM4793204: zBr2dpf4 S2; Danio rerio; RNA Seq	GSM4793204		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793204	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf4 S2 L004 I1 001.fastq.gz read2PairFiles=zBr2dpf4 S2 L004 R1 001.fastq.gz read3PairFiles=zBr2dpf4 S2 L004 R2 001.fastq.gz	zBr2dpf4_S2_L004_I1_001.fastq.gz zBr2dpf4_S2_L004_R1_001.fastq.gz zBr2dpf4_S2_L004_R2_001.fastq.gz	fastq fastq fastq	1188718016.0	12920848.0	GSM4793204 r4	0:8 1:26 2:58	A:317586867;C:263420618;G:296857671;T:310674373;N:178487	8	26	58		317586867	263420618	296857671	310674373	178487	SRX9142587	SRS7383891	SRA1127180	GEO	Harvard University	1	0.94167		0.10483		0.81602		0.49655		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61253	61253	SRR12661732	SRX9142586	SRS7383890	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf3 S1	GSM4793203		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf3 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793203	GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq	GSM4793203		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793203	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf3 S1 L001 I1 001.fastq.gz read2PairFiles=zBr2dpf3 S1 L001 R1 001.fastq.gz read3PairFiles=zBr2dpf3 S1 L001 R2 001.fastq.gz	zBr2dpf3_S1_L001_I1_001.fastq.gz zBr2dpf3_S1_L001_R1_001.fastq.gz zBr2dpf3_S1_L001_R2_001.fastq.gz	fastq fastq fastq	1226402964.0	13330467.0	GSM4793203 r1	0:8 1:26 2:58	A:326661734;C:276069009;G:303031527;T:320457713;N:182981	8	26	58		326661734	276069009	303031527	320457713	182981	SRX9142586	SRS7383890	SRA1127180	GEO	Harvard University	1	0.93957		0.09895		0.81337		0.4938		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61254	61254	SRR12661733	SRX9142586	SRS7383890	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf3 S1	GSM4793203		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf3 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793203	GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq	GSM4793203		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793203	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf3 S1 L002 I1 001.fastq.gz read2PairFiles=zBr2dpf3 S1 L002 R1 001.fastq.gz read3PairFiles=zBr2dpf3 S1 L002 R2 001.fastq.gz	zBr2dpf3_S1_L002_I1_001.fastq.gz zBr2dpf3_S1_L002_R1_001.fastq.gz zBr2dpf3_S1_L002_R2_001.fastq.gz	fastq fastq fastq	1210496624.0	13157572.0	GSM4793203 r2	0:8 1:26 2:58	A:323943138;C:272771349;G:297045042;T:316544450;N:192645	8	26	58		323943138	272771349	297045042	316544450	192645	SRX9142586	SRS7383890	SRA1127180	GEO	Harvard University	1	0.94096		0.09908		0.81416		0.50044		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61255	61255	SRR12661734	SRX9142586	SRS7383890	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf3 S1	GSM4793203		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf3 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793203	GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq	GSM4793203		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793203	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf3 S1 L003 I1 001.fastq.gz read2PairFiles=zBr2dpf3 S1 L003 R1 001.fastq.gz read3PairFiles=zBr2dpf3 S1 L003 R2 001.fastq.gz	zBr2dpf3_S1_L003_I1_001.fastq.gz zBr2dpf3_S1_L003_R1_001.fastq.gz zBr2dpf3_S1_L003_R2_001.fastq.gz	fastq fastq fastq	1199729404.0	13040537.0	GSM4793203 r3	0:8 1:26 2:58	A:321141508;C:269565671;G:294529755;T:314294746;N:197724	8	26	58		321141508	269565671	294529755	314294746	197724	SRX9142586	SRS7383890	SRA1127180	GEO	Harvard University	1	0.94108		0.102		0.81606		0.49463		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61256	61256	SRR12661735	SRX9142586	SRS7383890	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf3 S1	GSM4793203		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf3 S1	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793203	GSM4793203: zBr2dpf3 S1; Danio rerio; RNA Seq	GSM4793203		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793203	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf3 S1 L004 I1 001.fastq.gz read2PairFiles=zBr2dpf3 S1 L004 R1 001.fastq.gz read3PairFiles=zBr2dpf3 S1 L004 R2 001.fastq.gz	zBr2dpf3_S1_L004_I1_001.fastq.gz zBr2dpf3_S1_L004_R1_001.fastq.gz zBr2dpf3_S1_L004_R2_001.fastq.gz	fastq fastq fastq	1182541780.0	12853715.0	GSM4793203 r4	0:8 1:26 2:58	A:317147535;C:266216608;G:289343448;T:309653687;N:180502	8	26	58		317147535	266216608	289343448	309653687	180502	SRX9142586	SRS7383890	SRA1127180	GEO	Harvard University	1	0.94152		0.10077		0.81639		0.48378		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61257	61257	SRR12661728	SRX9142585	SRS7383889	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf2 S4	GSM4793202		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793202	GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq	GSM4793202		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793202	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf2 S4 L001 I1 001.fastq.gz read2PairFiles=zBr2dpf2 S4 L001 R1 001.fastq.gz read3PairFiles=zBr2dpf2 S4 L001 R2 001.fastq.gz	zBr2dpf2_S4_L001_I1_001.fastq.gz zBr2dpf2_S4_L001_R1_001.fastq.gz zBr2dpf2_S4_L001_R2_001.fastq.gz	fastq fastq fastq	2354711480.0	25594690.0	GSM4793202 r1	0:8 1:26 2:58	A:638596344;C:520071032;G:581522367;T:613545955;N:975782	8	26	58		638596344	520071032	581522367	613545955	975782	SRX9142585	SRS7383889	SRA1127180	GEO	Harvard University	1	0.93747		0.12301		0.81274		0.50067		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System
61258	61258	SRR12661729	SRX9142585	SRS7383889	SRP282920	PRJNA664124	Emergence of neuronal diversity during vertebrate brain development	GSE158142	Transcriptome Analysis	Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated but the landscape of transcriptional changes underlying brain development are poorly characterized. Here we describe a developmental single cell RNA seq catalog of 220 000 zebrafish brain cells encompassing 12 stages from 12 hpf to 15 dpf We characterize known and novel gene markers for 800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9 edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post embryonic stages. Reconstruction of cell specification trajectories reveals that late stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis. Overall design: 10X Genomics v2 scRNA seq libraries and scGESTALT		pubmed:33068532		zBr2dpf2 S4	GSM4793202		source name:zebrafish brain\|tissue:brain\|developmental stage:2dpf	zBr2dpf2 S4	Single cell RNA Sequencing data FASTQ files were processed using Cell Ranger v2.0.2 to generate count matrices Transcriptome libraries were mapped to a zebrafish reference built from a custom GTF file and the zebrafish GRCz10 release 86 genome assembly. File uploaded as Danio rerio.GRCz10.86.modified.gtf.gz. Some libraries were sequenced twice as technical replicates marked as b in raw files and the processing was done using the combination of all data processed data files have comb prefix scGESTALT libraries were processed using a custom pipeline available at https://github.com/shendurelab/Cas9FateMapping Genome build: GRCz10 Supplementary files format and content: barcodes.tsv files contain 10X Genomics cell barcodes genes.tsv files contain gene names matrix.mtx contain transcriptome count data web summary.html contain summary statistics for transcript mapping .rds files are the processed R objects .txt files contain marker genes identified for each cluster in the dataset URD.rds files are the processed R objects for performing URD cell trajectory analysis. tree.rds files are the final URD objects with cell trajectory trees for the retina and hypothalamus. Supplementary files format and content: scGESTALT data: Gest zBr15dpf8 and Gest zBr15dpf9 correspond to two samples from the same zebrafish ZF1. Gest zBr15dpf10 and Gest zBr15dpf11 correspond to two samples from the same zebrafish ZF2. Gest zBr15dpf12 and Gest zBr15dpf13 correspond to two samples from the same zebrafish ZF3. Gest zBr15dpf14 and Gest zBr15dpf15 correspond to two samples from the same zebrafish ZF4. Supplementary files format and content: scGESTALT data: *GestMaster.txt contains the 10X Genmoics cell identifiers CellBarcode and CellUMI that were used to matchlineage barcodes to transcriptomes. They also contain lineage barcode sequences HMID column the t SNE cluster membership number ClusterIdent column and unique identifier Readname. zfAllMerge FILTEREDUSEME.xlsx contains the merged statistics of all samples filtered to cont…	zebrafish brain		Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing		tissue:brain\|developmental stage:2dpf	GSM4793202	GSM4793202: zBr2dpf2 S4; Danio rerio; RNA Seq	GSM4793202		1	Libraries were prepared as described in manufacturer's protocol for v2 kits Single cell suspensions were processed through 10X Genomics v2 kits according to manufacturer's protocol to generate single cell cDNA libraries and prepared for sequencing	GEO Accession:GSM4793202	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP282920		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=zBr2dpf2 S4 L002 I1 001.fastq.gz read2PairFiles=zBr2dpf2 S4 L002 R1 001.fastq.gz read3PairFiles=zBr2dpf2 S4 L002 R2 001.fastq.gz	zBr2dpf2_S4_L002_I1_001.fastq.gz zBr2dpf2_S4_L002_R1_001.fastq.gz zBr2dpf2_S4_L002_R2_001.fastq.gz	fastq fastq fastq	2408983200.0	26184600.0	GSM4793202 r2	0:8 1:26 2:58	A:651954485;C:532609422;G:598183054;T:625305824;N:930415	8	26	58		651954485	532609422	598183054	625305824	930415	SRX9142585	SRS7383889	SRA1127180	GEO	Harvard University	1	0.93328		0.11839		0.80687		0.5125		58		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-09-17	Hatching	Embryo	Brain	Nervous System

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");;