metadata: run_metadata: 1,515 rows where devstage_curation = "Larval" and technology = "10x"

1,515 rows where devstage_curation = "Larval" 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.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
10176	10176	ERR5858457	ERX5504346	ERS6343450	ERP128749	PRJEB44676	scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	E-MTAB-10390	Transcriptome Analysis	To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals.	ENA FIRST PUBLIC:2021 05 24\|ENA LAST UPDATE:2021 05 24		Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.	Naive	SAMEA8658904	University Of Edinburgh	ENA first public:2021 05 24\|ENA last update:2021 05 24\|External Id:SAMEA8658904\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 05 24T00:14:32Z\|INSDC last update:2021 05 24T00:14:32Z\|INSDC status:public\|Submitter Id:E MTAB 10390:Naive\|age:4\|broker name:ArrayExpress\|cell type:ependymo radial glial cell\|common name:zebrafish\|developmental stage:larval day 4\|immunophenotype:Her4.3+ positive\|organism part:spinal cord\|sample name:E MTAB 10390:Naive\|sex:mixed\|strain:WIK								Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord	E MTAB 10390:Naive p	Naive p	scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128749	Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	ENA FIRST PUBLIC:2021 05 24\|ENA LAST UPDATE:2021 05 24	Naive.bam	bam	44972162730.0	499690697.0	E MTAB 10390:Naive	0:90	A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100	90				13658826375	8733304343	9348137569	13228064343	3830100	ERX5504346	ERS6343450	ERA4142789	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	1	0.89428		0.32693		0.75276		0.5314		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-05-24	Larval	Larval	Spinal Cord	Nervous System
10177	10177	ERR5858456	ERX5504345	ERS6343449	ERP128749	PRJEB44676	scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	E-MTAB-10390	Transcriptome Analysis	To analyse lesion induced gene regulation in progenitor cells at single cell resolution we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals.	ENA FIRST PUBLIC:2021 05 24\|ENA LAST UPDATE:2021 05 24		Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.	Lesi1d	SAMEA8658903	University Of Edinburgh	ENA first public:2021 05 24\|ENA last update:2021 05 24\|External Id:SAMEA8658903\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 05 24T00:14:32Z\|INSDC last update:2021 05 24T00:14:32Z\|INSDC status:public\|Submitter Id:E MTAB 10390:Lesi1d\|age:4\|broker name:ArrayExpress\|cell type:ependymo radial glial cell\|common name:zebrafish\|developmental stage:larval day 4\|immunophenotype:Her4.3+ positive\|injury:spinal injury lesion\|organism part:spinal cord\|sample name:E MTAB 10390:Lesi1d\|sex:mixed\|strain:WIK								Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord	E MTAB 10390:Lesioned p	Lesioned p	scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.	Experimental Factor: injury:spinal injury lesion	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP128749	Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord	ENA FIRST PUBLIC:2021 05 24\|ENA LAST UPDATE:2021 05 24	Lesioned.bam	bam	49902588630.0	554473207.0	E MTAB 10390:Lesioned	0:90	A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526	90				14713351178	10191139050	10897887675	14095967201	4243526	ERX5504345	ERS6343449	ERA4142789	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	1	0.91197		0.29137		0.7568		0.56523		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-05-24	Larval	Larval	Spinal Cord	Nervous System
10186	10186	ERR6212423	ERX5847531	ERS7094943	ERP130388	PRJEB46176	scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	E-MTAB-10379_3	Transcriptome Analysis	To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals.	ENA FIRST PUBLIC:2021 07 08\|ENA LAST UPDATE:2021 07 08		Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines	Naive	SAMEA9361876	University Of Edinburgh	ENA first public:2021 07 08\|ENA last update:2021 07 08\|External Id:SAMEA9361876\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 07 08T11:18:57Z\|INSDC last update:2021 07 08T11:18:57Z\|INSDC status:public\|Submitter Id:E MTAB 10379 3:Naive\|age:4\|broker name:ArrayExpress\|cell type:mixed macrophage and microglia\|common name:zebrafish\|developmental stage:larval day 4\|immunophenotype:mpeg1.1 positive\|organism part:spinal cord\|sample name:E MTAB 10379 3:Naive\|sex:mixed\|strain:WIK								Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord	E MTAB 10379 3:Naive p	Naive p	scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP130388	Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	ENA FIRST PUBLIC:2021 07 08\|ENA LAST UPDATE:2021 07 08	Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz	fastq fastq fastq	60168324125.0	481346593.0	E MTAB 10379 3:Naive	0:8 1:27 2:90	A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241	8	27	90		12424400694	9366563781	10029312355	11497237299	3679241	ERX5847531	ERS7094943	ERA5186263	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	1	0.94834		0.09482		0.802		0.5277		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-07-08	Larval	Larval	Multi-tissue	Multi-system
10187	10187	ERR6212422	ERX5847530	ERS7094942	ERP130388	PRJEB46176	scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	E-MTAB-10379_3	Transcriptome Analysis	To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf compared to age matched uninjured animals.	ENA FIRST PUBLIC:2021 07 08\|ENA LAST UPDATE:2021 07 08		Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines	Lesi1d	SAMEA9361875	University Of Edinburgh	ENA first public:2021 07 08\|ENA last update:2021 07 08\|External Id:SAMEA9361875\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 07 08T11:18:57Z\|INSDC last update:2021 07 08T11:18:57Z\|INSDC status:public\|Submitter Id:E MTAB 10379 3:Lesi1d\|age:4\|broker name:ArrayExpress\|cell type:mixed macrophage and microglia\|common name:zebrafish\|developmental stage:larval day 4\|immunophenotype:mpeg1.1 positive\|injury:spinal cord lesion\|organism part:spinal cord\|sample name:E MTAB 10379 3:Lesi1d\|sex:mixed\|strain:WIK								Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord	E MTAB 10379 3:Lesioned p	Lesioned p	scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines	Experimental Factor: injury:spinal cord lesion	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP130388	Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord	ENA FIRST PUBLIC:2021 07 08\|ENA LAST UPDATE:2021 07 08	Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz	fastq fastq fastq	61701873000.0	493614984.0	E MTAB 10379 3:Lesioned	0:8 1:27 2:90	A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277	8	27	90		12952533019	9222397450	9920185920	12326470894	3761277	ERX5847530	ERS7094942	ERA5186263	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	1	0.93082		0.10862		0.80302		0.54924		90		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United Kingdom	2021-07-08	Larval	Larval	Multi-tissue	Multi-system
11134	11134	ERR9981089	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23		Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP								Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz	fastq fastq	60177283876.0	509976982.0	E MTAB 11991:P25452 2002 S2 L001	0:28 1:90	A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481	28	90			17254566438	13547211711	14188233429	15185192817	2079481	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00671	0.93031	0.00231	0.11028	0.9932	0.82227	0.30887	0.58272	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11135	11135	ERR9981090	ERX9522049	ERS12503451	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23		Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 1 lck control	SAMEA110406305	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406305\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 1 lck control\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 1 lck control\|strain:Tglck:GFP								Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 1 lck control p	Sample 1 lck control p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:n1	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz	fastq fastq	60597886144.0	513541408.0	E MTAB 11991:P25452 2002 S2 L002	0:28 1:90	A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626	28	90			17368154358	13649089056	14296037620	15282869484	1735626	ERX9522049	ERS12503451	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00656	0.92899	0.00211	0.11059	0.99334	0.82335	0.32311	0.57644	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11136	11136	ERR9981087	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23		Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP								Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz	fastq fastq	20866120186.0	176831527.0	E MTAB 11991:P25452 2001 S1 L001	0:28 1:90	A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046	28	90			5933525376	4737179804	5025711080	5168983880	720046	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00805	0.92622	0.00259	0.11842	0.99302	0.83027	0.2729	0.57699	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
11137	11137	ERR9981088	ERX9522048	ERS12503450	ERP139797	PRJEB54930	Single cell RNA sequencing of lck GFP transgenic zebrafish	E-MTAB-11991	Transcriptome Analysis	The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23		Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing u…	Sample 2 lck GO+BA	SAMEA110406304	Institute of Environmental Medicine, Karolinska Institutet	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23\|External Id:SAMEA110406304\|INSDC center alias:Institute of Environmental Medicine Karolinska Institutet\|INSDC center name:Institute of Environmental Medicine Karolinska Institutet\|INSDC first public:2022 07 23T04:33:35Z\|INSDC last update:2022 07 23T04:33:35Z\|INSDC status:public\|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larva\|disease:normal\|genotype:wild type genotype\|isolate:not applicable\|organism part:whole organism\|sample name:E MTAB 11991:Sample 2 lck GO+BA\|strain:Tglck:GFP								Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	E MTAB 11991:Sample 2 lck GO+BA p	Sample 2 lck GO+BA p	Single cell RNA sequencing of lck GFP transgenic zebrafish	The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief 2 hpf embryos were transferred to petri dishes with sterile E3 medium supplemented with ampicillin 100 μg/mL kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium transferred to flasks and incubated at 28°C. The viability was monitored and sterile medium was refreshed daily. At day 4 the hatched embryos were used for the sterility validation. A day 5 germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate four replicates i.e. two hundred larvae in total were used for each condition. post the exposure zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly zebrafish larvae were euthanized with 0.01% of tricaine for 5 min collected in 1.5 mL tube and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh with an additional washing using DMEM w…	Experimental Factor: stimulus:graphene oxide 30 microgram per milliliter\|Experimental Factor: compound:butyrate\|Experimental Factor: dose:2.5	AMPLICON	TRANSCRIPTOMIC SINGLE CELL	size fractionation	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP139797	Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish	ENA FIRST PUBLIC:2022 07 23\|ENA LAST UPDATE:2022 07 23	P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz	fastq fastq	21068682172.0	178548154.0	E MTAB 11991:P25452 2001 S1 L002	0:28 1:90	A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528	28	90			5987758267	4786100132	5078292970	5215926275	604528	ERX9522048	ERS12503450	ERA16488297	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	Institute of Environmental Medicine, Karolinska Institutet\|European Nucleotide Archive	2	0.00813	0.92702	0.00264	0.11874	0.99283	0.82737	0.30228	0.56929	28	90	T	B	sc-like readlen	illumina	novaseq_era	full_length	size_fractionation	trueseq	sc	single_cell_droplet	10x	Sweden	2022-07-23	Larval	Larval	Whole Organism	All anatomical structures
24790	24790	SRR25509944	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S17_L001_R2_001.fastq.gz 5DPF_WT_plus_S17_L001_R1_001.fastq.gz 5DPF_WT_plus_S17_L001_I1_001.fastq.gz	fastq fastq fastq	5999080077.0	47236851.0	GSM7680083 r1	0:8 1:28 2:91	A:1212144705;C:959823109;G:1045323833;T:1081182723;N:79071	8	28	91		1212144705	959823109	1045323833	1081182723	79071	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91673		0.11695		0.77481		0.51165		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24791	24791	SRR25509945	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S17_L002_R2_001.fastq.gz 5DPF_WT_plus_S17_L002_R1_001.fastq.gz 5DPF_WT_plus_S17_L002_I1_001.fastq.gz	fastq fastq fastq	6012350180.0	47341340.0	GSM7680083 r2	0:8 1:28 2:91	A:1215185110;C:961739027;G:1047332997;T:1083733742;N:71064	8	28	91		1215185110	961739027	1047332997	1083733742	71064	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91842		0.11714		0.7763		0.51731		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24792	24792	SRR25509946	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S18_L001_R2_001.fastq.gz 5DPF_WT_plus_S18_L001_R1_001.fastq.gz 5DPF_WT_plus_S18_L001_I1_001.fastq.gz	fastq fastq fastq	4990947473.0	39298799.0	GSM7680083 r3	0:8 1:28 2:91	A:1007619958;C:800073636;G:871756682;T:896670984;N:69449	8	28	91		1007619958	800073636	871756682	896670984	69449	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91717		0.11737		0.7767		0.51879		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24793	24793	SRR25509947	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S18_L002_I1_001.fastq.gz 5DPF_WT_plus_S18_L002_R1_001.fastq.gz 5DPF_WT_plus_S18_L002_R2_001.fastq.gz	fastq fastq fastq	4994343707.0	39325541.0	GSM7680083 r4	0:8 1:28 2:91	A:1008545361;C:800479170;G:872044753;T:897494026;N:60921	8	28	91		1008545361	800479170	872044753	897494026	60921	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.9173		0.11671		0.778		0.51414		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24794	24794	SRR25509948	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S20_L001_R2_001.fastq.gz 5DPF_WT_plus_S20_L001_R1_001.fastq.gz 5DPF_WT_plus_S20_L001_I1_001.fastq.gz	fastq fastq fastq	4150807675.0	32683525.0	GSM7680083 r7	0:8 1:28 2:91	A:839301254;C:665476121;G:723277159;T:746089009;N:57232	8	28	91		839301254	665476121	723277159	746089009	57232	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91704		0.11665		0.77589		0.51231		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24795	24795	SRR25509949	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S20_L002_R2_001.fastq.gz 5DPF_WT_plus_S20_L002_R1_001.fastq.gz 5DPF_WT_plus_S20_L002_I1_001.fastq.gz	fastq fastq fastq	4152701499.0	32698437.0	GSM7680083 r8	0:8 1:28 2:91	A:839837413;C:665793367;G:723399518;T:746476220;N:51249	8	28	91		839837413	665793367	723399518	746476220	51249	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91769		0.11677		0.77473		0.5172		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24796	24796	SRR25510006	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S19_L001_I1_001.fastq.gz 5DPF_WT_plus_S19_L001_R1_001.fastq.gz 5DPF_WT_plus_S19_L001_R2_001.fastq.gz	fastq fastq fastq	5570139228.0	43859364.0	GSM7680083 r5	0:8 1:28 2:91	A:1124433319;C:892106407;G:974065175;T:1000519772;N:77451	8	28	91		1124433319	892106407	974065175	1000519772	77451	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.9181		0.11708		0.77725		0.506		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24797	24797	SRR25510007	SRX21240524	SRS18495447	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 prdm16:gal4UASGFP + 5dpf scRNAseq	GSM7680083		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680083	GSM7680083: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680083 r1	GSM7680083	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	5DPF_WT_plus_S19_L002_R2_001.fastq.gz 5DPF_WT_plus_S19_L002_R1_001.fastq.gz 5DPF_WT_plus_S19_L002_I1_001.fastq.gz	fastq fastq fastq	5568879134.0	43849442.0	GSM7680083 r6	0:8 1:28 2:91	A:1124462080;C:891765530;G:973382320;T:1000621312;N:67980	8	28	91		1124462080	891765530	973382320	1000621312	67980	SRX21240524	SRS18495447	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91836		0.11752		0.77786		0.49118		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24798	24798	SRR25509950	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S29_L001_I1_001.fastq.gz MECOM_minus_S29_L001_R1_001.fastq.gz MECOM_minus_S29_L001_R2_001.fastq.gz	fastq fastq fastq	6472457718.0	50964234.0	GSM7680088 r1	0:8 1:28 2:91	A:1374177983;C:969847712;G:1063043909;T:1230585953;N:89737	8	28	91		1374177983	969847712	1063043909	1230585953	89737	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91899		0.23002		0.75597		0.50918		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24799	24799	SRR25509951	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S29_L002_I1_001.fastq.gz MECOM_minus_S29_L002_R1_001.fastq.gz MECOM_minus_S29_L002_R2_001.fastq.gz	fastq fastq fastq	6479801747.0	51022061.0	GSM7680088 r2	0:8 1:28 2:91	A:1375879660;C:970771702;G:1064110805;T:1232166662;N:78722	8	28	91		1375879660	970771702	1064110805	1232166662	78722	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91932		0.23011		0.75666		0.50726		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24800	24800	SRR25509952	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S30_L001_I1_001.fastq.gz MECOM_minus_S30_L001_R1_001.fastq.gz MECOM_minus_S30_L001_R2_001.fastq.gz	fastq fastq fastq	6055044278.0	47677514.0	GSM7680088 r3	0:8 1:28 2:91	A:1285162347;C:907248700;G:995411468;T:1150745942;N:85317	8	28	91		1285162347	907248700	995411468	1150745942	85317	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91771		0.2306		0.75799		0.51641		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24801	24801	SRR25509953	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S30_L002_I1_001.fastq.gz MECOM_minus_S30_L002_R1_001.fastq.gz MECOM_minus_S30_L002_R2_001.fastq.gz	fastq fastq fastq	6065969453.0	47763539.0	GSM7680088 r4	0:8 1:28 2:91	A:1287814805;C:908939739;G:996849881;T:1152803356;N:74268	8	28	91		1287814805	908939739	996849881	1152803356	74268	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91856		0.23244		0.75844		0.51273		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24802	24802	SRR25509954	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S31_L001_I1_001.fastq.gz MECOM_minus_S31_L001_R1_001.fastq.gz MECOM_minus_S31_L001_R2_001.fastq.gz	fastq fastq fastq	5279309101.0	41569363.0	GSM7680088 r5	0:8 1:28 2:91	A:1122213686;C:789300425;G:868235888;T:1002988275;N:73759	8	28	91		1122213686	789300425	868235888	1002988275	73759	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91638		0.23107		0.75795		0.51508		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24803	24803	SRR25509955	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S31_L002_I1_001.fastq.gz MECOM_minus_S31_L002_R1_001.fastq.gz MECOM_minus_S31_L002_R2_001.fastq.gz	fastq fastq fastq	5282579605.0	41595115.0	GSM7680088 r6	0:8 1:28 2:91	A:1123052612;C:789776127;G:868371205;T:1003891470;N:64051	8	28	91		1123052612	789776127	868371205	1003891470	64051	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91687		0.23155		0.75653		0.51167		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24804	24804	SRR25509956	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S32_L001_I1_001.fastq.gz MECOM_minus_S32_L001_R1_001.fastq.gz MECOM_minus_S32_L001_R2_001.fastq.gz	fastq fastq fastq	5155833986.0	40597118.0	GSM7680088 r7	0:8 1:28 2:91	A:1096166065;C:771837218;G:846468036;T:979794053;N:72366	8	28	91		1096166065	771837218	846468036	979794053	72366	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91864		0.23062		0.75783		0.5144		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24805	24805	SRR25509957	SRX21240523	SRS18495446	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 prdm16:gal4UASGFP mecom / 5dpf scRNAseq	GSM7680088		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680088	GSM7680088: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680088 r1	GSM7680088	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	MECOM_minus_S32_L002_I1_001.fastq.gz MECOM_minus_S32_L002_R1_001.fastq.gz MECOM_minus_S32_L002_R2_001.fastq.gz	fastq fastq fastq	5158852395.0	40620885.0	GSM7680088 r8	0:8 1:28 2:91	A:1096925078;C:772260867;G:846795917;T:980455576;N:63097	8	28	91		1096925078	772260867	846795917	980455576	63097	SRX21240523	SRS18495446	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91859		0.23143		0.75921		0.51192		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24806	24806	SRR25509958	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S1_L001_I1_001.fastq.gz PRDM16-GFP_S1_L001_R1_001.fastq.gz PRDM16-GFP_S1_L001_R2_001.fastq.gz	fastq fastq fastq	7339736654.0	57793202.0	GSM7680087 r1	0:8 1:28 2:91	A:1557377528;C:1077119414;G:1156228317;T:1468352980;N:103143	8	28	91		1557377528	1077119414	1156228317	1468352980	103143	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91516		0.25902		0.74255		0.49922		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24807	24807	SRR25509959	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S1_L002_I1_001.fastq.gz PRDM16-GFP_S1_L002_R1_001.fastq.gz PRDM16-GFP_S1_L002_R2_001.fastq.gz	fastq fastq fastq	7410090336.0	58347168.0	GSM7680087 r2	0:8 1:28 2:91	A:1569421640;C:1090998538;G:1171253819;T:1477822651;N:95640	8	28	91		1569421640	1090998538	1171253819	1477822651	95640	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91462		0.25846		0.74215		0.49672		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24808	24808	SRR25509960	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S2_L001_I1_001.fastq.gz PRDM16-GFP_S2_L001_R1_001.fastq.gz PRDM16-GFP_S2_L001_R2_001.fastq.gz	fastq fastq fastq	7620847217.0	60006671.0	GSM7680087 r3	0:8 1:28 2:91	A:1615026295;C:1121044318;G:1201364994;T:1523062938;N:108516	8	28	91		1615026295	1121044318	1201364994	1523062938	108516	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91495		0.26021		0.74188		0.49871		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24809	24809	SRR25509961	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S2_L002_I1_001.fastq.gz PRDM16-GFP_S2_L002_R1_001.fastq.gz PRDM16-GFP_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7658170739.0	60300557.0	GSM7680087 r4	0:8 1:28 2:91	A:1620018228;C:1130072970;G:1211145212;T:1526013817;N:100460	8	28	91		1620018228	1130072970	1211145212	1526013817	100460	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.9153		0.25733		0.74406		0.49822		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24810	24810	SRR25509962	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S3_L001_I1_001.fastq.gz PRDM16-GFP_S3_L001_R1_001.fastq.gz PRDM16-GFP_S3_L001_R2_001.fastq.gz	fastq fastq fastq	7520150568.0	59213784.0	GSM7680087 r5	0:8 1:28 2:91	A:1592224470;C:1104917106;G:1187483622;T:1503722424;N:106722	8	28	91		1592224470	1104917106	1187483622	1503722424	106722	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91528		0.25852		0.74168		0.50087		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24811	24811	SRR25509963	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S3_L002_I1_001.fastq.gz PRDM16-GFP_S3_L002_R1_001.fastq.gz PRDM16-GFP_S3_L002_R2_001.fastq.gz	fastq fastq fastq	7547416198.0	59428474.0	GSM7680087 r6	0:8 1:28 2:91	A:1595335949;C:1112405532;G:1195632258;T:1504519719;N:97676	8	28	91		1595335949	1112405532	1195632258	1504519719	97676	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91572		0.25684		0.74227		0.49429		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24812	24812	SRR25509964	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S4_L001_I1_001.fastq.gz PRDM16-GFP_S4_L001_R1_001.fastq.gz PRDM16-GFP_S4_L001_R2_001.fastq.gz	fastq fastq fastq	6203887389.0	48849507.0	GSM7680087 r7	0:8 1:28 2:91	A:1315023626;C:910416020;G:979167464;T:1240610297;N:87730	8	28	91		1315023626	910416020	979167464	1240610297	87730	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91294		0.25905		0.74426		0.49642		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24813	24813	SRR25509965	SRX21240522	SRS18495445	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 prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq	GSM7680087		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680087	GSM7680087: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680087 r1	GSM7680087	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	PRDM16-GFP_S4_L002_I1_001.fastq.gz PRDM16-GFP_S4_L002_R1_001.fastq.gz PRDM16-GFP_S4_L002_R2_001.fastq.gz	fastq fastq fastq	6164249419.0	48537397.0	GSM7680087 r8	0:8 1:28 2:91	A:1303982345;C:907803673;G:976227040;T:1228810005;N:80064	8	28	91		1303982345	907803673	976227040	1228810005	80064	SRX21240522	SRS18495445	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91422		0.25666		0.74383		0.49596		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24814	24814	SRR25509966	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S25_L001_I1_001.fastq.gz MECOM_plus_S25_L001_R1_001.fastq.gz MECOM_plus_S25_L001_R2_001.fastq.gz	fastq fastq fastq	2154821446.0	16967098.0	GSM7680086 r1	0:8 1:28 2:91	A:451330902;C:339756831;G:379343350;T:373544930;N:29905	8	28	91		451330902	339756831	379343350	373544930	29905	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91882		0.142		0.78299		0.51956		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24815	24815	SRR25509967	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S25_L002_I1_001.fastq.gz MECOM_plus_S25_L002_R1_001.fastq.gz MECOM_plus_S25_L002_R2_001.fastq.gz	fastq fastq fastq	2158219204.0	16993852.0	GSM7680086 r2	0:8 1:28 2:91	A:452280625;C:340228509;G:379707034;T:374197697;N:26667	8	28	91		452280625	340228509	379707034	374197697	26667	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91895		0.1417		0.78279		0.51981		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24816	24816	SRR25509968	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S26_L001_I1_001.fastq.gz MECOM_plus_S26_L001_R1_001.fastq.gz MECOM_plus_S26_L001_R2_001.fastq.gz	fastq fastq fastq	2361287251.0	18592813.0	GSM7680086 r3	0:8 1:28 2:91	A:492891294;C:373079069;G:416862992;T:409079819;N:32809	8	28	91		492891294	373079069	416862992	409079819	32809	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.92068		0.13997		0.78516		0.50532		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24817	24817	SRR25509969	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S26_L002_I1_001.fastq.gz MECOM_plus_S26_L002_R1_001.fastq.gz MECOM_plus_S26_L002_R2_001.fastq.gz	fastq fastq fastq	2362115545.0	18599335.0	GSM7680086 r4	0:8 1:28 2:91	A:493282758;C:373220256;G:416785305;T:409222388;N:28778	8	28	91		493282758	373220256	416785305	409222388	28778	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.92013		0.14129		0.78468		0.52049		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24818	24818	SRR25509970	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S27_L001_I1_001.fastq.gz MECOM_plus_S27_L001_R1_001.fastq.gz MECOM_plus_S27_L001_R2_001.fastq.gz	fastq fastq fastq	2093107066.0	16481158.0	GSM7680086 r5	0:8 1:28 2:91	A:438295698;C:330083473;G:369094473;T:362282989;N:28745	8	28	91		438295698	330083473	369094473	362282989	28745	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91759		0.13991		0.78354		0.51917		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24819	24819	SRR25509971	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S27_L002_R2_001.fastq.gz MECOM_plus_S27_L002_R1_001.fastq.gz MECOM_plus_S27_L002_I1_001.fastq.gz	fastq fastq fastq	2095025401.0	16496263.0	GSM7680086 r6	0:8 1:28 2:91	A:438926470;C:330300198;G:369243520;T:362664613;N:25132	8	28	91		438926470	330300198	369243520	362664613	25132	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91795		0.14216		0.78151		0.5067		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24820	24820	SRR25509972	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S28_L001_R2_001.fastq.gz MECOM_plus_S28_L001_R1_001.fastq.gz MECOM_plus_S28_L001_I1_001.fastq.gz	fastq fastq fastq	1722573390.0	13563570.0	GSM7680086 r7	0:8 1:28 2:91	A:360865837;C:272246731;G:303643951;T:297504190;N:24161	8	28	91		360865837	272246731	303643951	297504190	24161	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91897		0.13999		0.78648		0.49913		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24821	24821	SRR25509973	SRX21240521	SRS18495444	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 prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq	GSM7680086		source name:tail\|tissue:tail\|genotype:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf 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:olig2dsRed mecom / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680086	GSM7680086: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP+ mecom / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680086 r1	GSM7680086	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	MECOM_plus_S28_L002_I1_001.fastq.gz MECOM_plus_S28_L002_R1_001.fastq.gz MECOM_plus_S28_L002_R2_001.fastq.gz	fastq fastq fastq	1724036303.0	13575089.0	GSM7680086 r8	0:8 1:28 2:91	A:361391368;C:272402118;G:303699423;T:297819212;N:20978	8	28	91		361391368	272402118	303699423	297819212	20978	SRX21240521	SRS18495444	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.92182		0.14094		0.78326		0.50699		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24822	24822	SRR25509974	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S5_L001_R2_001.fastq.gz PRDM16plusGFP_S5_L001_R1_001.fastq.gz PRDM16plusGFP_S5_L001_I1_001.fastq.gz	fastq fastq fastq	8567717053.0	67462339.0	GSM7680085 r1	0:8 1:28 2:91	A:1758073165;C:1341216272;G:1446728174;T:1592934812;N:120426	8	28	91		1758073165	1341216272	1446728174	1592934812	120426	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.90663		0.17669		0.75812		0.50234		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24823	24823	SRR25509975	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S5_L002_R2_001.fastq.gz PRDM16plusGFP_S5_L002_R1_001.fastq.gz PRDM16plusGFP_S5_L002_I1_001.fastq.gz	fastq fastq fastq	8694310526.0	68459138.0	GSM7680085 r2	0:8 1:28 2:91	A:1780912602;C:1365177337;G:1472402153;T:1611176829;N:112637	8	28	91		1780912602	1365177337	1472402153	1611176829	112637	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.90543		0.17508		0.76019		0.51005		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24824	24824	SRR25509976	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S6_L001_R2_001.fastq.gz PRDM16plusGFP_S6_L001_R1_001.fastq.gz PRDM16plusGFP_S6_L001_I1_001.fastq.gz	fastq fastq fastq	9112215456.0	71749728.0	GSM7680085 r3	0:8 1:28 2:91	A:1868388882;C:1426817380;G:1540502920;T:1693385950;N:130116	8	28	91		1868388882	1426817380	1540502920	1693385950	130116	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.90763		0.17756		0.76102		0.50457		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24825	24825	SRR25509977	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S6_L002_I1_001.fastq.gz PRDM16plusGFP_S6_L002_R1_001.fastq.gz PRDM16plusGFP_S6_L002_R2_001.fastq.gz	fastq fastq fastq	9170568781.0	72209203.0	GSM7680085 r4	0:8 1:28 2:91	A:1876786596;C:1440704341;G:1555176461;T:1698251178;N:118897	8	28	91		1876786596	1440704341	1555176461	1698251178	118897	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.9062		0.17617		0.76203		0.49732		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24826	24826	SRR25509978	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S7_L001_R2_001.fastq.gz PRDM16plusGFP_S7_L001_R1_001.fastq.gz PRDM16plusGFP_S7_L001_I1_001.fastq.gz	fastq fastq fastq	96282510.0	758130.0	GSM7680085 r5	0:8 1:28 2:91	A:19884451;C:15070058;G:16206702;T:17827293;N:1326	8	28	91		19884451	15070058	16206702	17827293	1326	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.76071		0.14671		0.78064		0.49267		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24827	24827	SRR25509979	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S7_L002_I1_001.fastq.gz PRDM16plusGFP_S7_L002_R2_001.fastq.gz PRDM16plusGFP_S7_L002_R1_001.fastq.gz	fastq fastq fastq	96503236.0	759868.0	GSM7680085 r6	0:8 1:28 2:91	A:19898524;C:15152212;G:16290226;T:17805918;N:1108	8	28	91		19898524	15152212	16290226	17805918	1108	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.76382		0.1467		0.78508		0.48995		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24828	24828	SRR25509980	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S8_L001_I1_001.fastq.gz PRDM16plusGFP_S8_L001_R1_001.fastq.gz PRDM16plusGFP_S8_L001_R2_001.fastq.gz	fastq fastq fastq	8873313978.0	69868614.0	GSM7680085 r7	0:8 1:28 2:91	A:1820893372;C:1390912026;G:1498935631;T:1647176605;N:126240	8	28	91		1820893372	1390912026	1498935631	1647176605	126240	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.90718		0.17603		0.76211		0.50458		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24829	24829	SRR25509981	SRX21240520	SRS18495443	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 prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq	GSM7680085		source name:tail\|tissue:tail\|genotype:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf 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:olig2dsRed prdm16 / prdm16:gal4UASGFP\|age:5dpf\|cell type:Spinal cord MNs	GSM7680085	GSM7680085: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP + prdm16 / 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680085 r1	GSM7680085	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	PRDM16plusGFP_S8_L002_I1_001.fastq.gz PRDM16plusGFP_S8_L002_R1_001.fastq.gz PRDM16plusGFP_S8_L002_R2_001.fastq.gz	fastq fastq fastq	8980314526.0	70711138.0	GSM7680085 r8	0:8 1:28 2:91	A:1839681468;C:1412028536;G:1521396962;T:1661490212;N:116380	8	28	91		1839681468	1412028536	1521396962	1661490212	116380	SRX21240520	SRS18495443	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.9078		0.17604		0.76037		0.47729		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24830	24830	SRR25509982	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S21_L001_I1_001.fastq.gz 5DPF_WT_minus_S21_L001_R1_001.fastq.gz 5DPF_WT_minus_S21_L001_R2_001.fastq.gz	fastq fastq fastq	8634577600.0	67988800.0	GSM7680084 r1	0:8 1:28 2:91	A:1833391508;C:1279550998;G:1408086737;T:1665829499;N:122058	8	28	91		1833391508	1279550998	1408086737	1665829499	122058	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.92		0.2485		0.75552		0.51753		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24831	24831	SRR25509983	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S21_L002_I1_001.fastq.gz 5DPF_WT_minus_S21_L002_R1_001.fastq.gz 5DPF_WT_minus_S21_L002_R2_001.fastq.gz	fastq fastq fastq	8644279892.0	68065196.0	GSM7680084 r2	0:8 1:28 2:91	A:1835831383;C:1280886675;G:1409188624;T:1667919807;N:106347	8	28	91		1835831383	1280886675	1409188624	1667919807	106347	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91942		0.24867		0.75396		0.52058		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24832	24832	SRR25509984	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S22_L001_R2_001.fastq.gz 5DPF_WT_minus_S22_L001_R1_001.fastq.gz 5DPF_WT_minus_S22_L001_I1_001.fastq.gz	fastq fastq fastq	6144243998.0	48379874.0	GSM7680084 r3	0:8 1:28 2:91	A:1307018689;C:910675193;G:999334562;T:1185454346;N:85744	8	28	91		1307018689	910675193	999334562	1185454346	85744	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91944		0.2505		0.75538		0.5154		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24833	24833	SRR25509985	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S22_L002_I1_001.fastq.gz 5DPF_WT_minus_S22_L002_R1_001.fastq.gz 5DPF_WT_minus_S22_L002_R2_001.fastq.gz	fastq fastq fastq	6161162938.0	48513094.0	GSM7680084 r4	0:8 1:28 2:91	A:1310818438;C:913067206;G:1001801994;T:1188928241;N:75675	8	28	91		1310818438	913067206	1001801994	1188928241	75675	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91847		0.24895		0.75483		0.52092		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24834	24834	SRR25509986	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S23_L001_I1_001.fastq.gz 5DPF_WT_minus_S23_L001_R1_001.fastq.gz 5DPF_WT_minus_S23_L001_R2_001.fastq.gz	fastq fastq fastq	6893652075.0	54280725.0	GSM7680084 r5	0:8 1:28 2:91	A:1466387768;C:1021460104;G:1123606745;T:1327994370;N:96988	8	28	91		1466387768	1021460104	1123606745	1327994370	96988	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.92042		0.24759		0.75663		0.51662		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24835	24835	SRR25509987	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S23_L002_R1_001.fastq.gz 5DPF_WT_minus_S23_L002_R2_001.fastq.gz 5DPF_WT_minus_S23_L002_I1_001.fastq.gz	fastq fastq fastq	6907881409.0	54392767.0	GSM7680084 r6	0:8 1:28 2:91	A:1469526451;C:1023529399;G:1125771813;T:1330830542;N:83592	8	28	91		1469526451	1023529399	1125771813	1330830542	83592	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91879		0.24904		0.75479		0.52175		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24836	24836	SRR25509988	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S24_L001_R2_001.fastq.gz 5DPF_WT_minus_S24_L001_R1_001.fastq.gz 5DPF_WT_minus_S24_L001_I1_001.fastq.gz	fastq fastq fastq	6155284362.0	48466806.0	GSM7680084 r7	0:8 1:28 2:91	A:1309788155;C:909805561;G:1001863122;T:1188939208;N:83300	8	28	91		1309788155	909805561	1001863122	1188939208	83300	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91932		0.252		0.7541		0.52096		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
24837	24837	SRR25509989	SRX21240519	SRS18495442	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 prdm16:gal4UASGFP 5dpf scRNAseq	GSM7680084		source name:tail\|tissue:tail\|genotype:olig2:dsRed prdm16gal4:UASGFP\|age:5dpf\|cell type:Spinal cord MNs\|geo loc name:missing\|collection date:missing	Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf 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:5dpf\|cell type:Spinal cord MNs	GSM7680084	GSM7680084: Spinal cord MNs olig2dsRed prdm16:gal4UASGFP 5dpf scRNAseq; Danio rerio; RNA Seq	GSM7680084 r1	GSM7680084	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	5DPF_WT_minus_S24_L002_I1_001.fastq.gz 5DPF_WT_minus_S24_L002_R1_001.fastq.gz 5DPF_WT_minus_S24_L002_R2_001.fastq.gz	fastq fastq fastq	6165991605.0	48551115.0	GSM7680084 r8	0:8 1:28 2:91	A:1312424825;C:911081786;G:1003163970;T:1191408145;N:72739	8	28	91		1312424825	911081786	1003163970	1191408145	72739	SRX21240519	SRS18495442	SRA1686067	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	Dasen, Neuroscience Institute, New York University Grossman School of Medicine	1	0.91842		0.24989		0.75542		0.51918		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-03	Larval	Larval	Tail	Multi-system
25237	25237	SRR25721801	SRX21445937	SRS18680715	SRP456253	PRJNA1007646	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]	GSE241296	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration…				zebrafish larva neurons and glia scRNAseq	GSM7720759		source name:zebrafish larva\|cell type:neurons and glia\|tissue:zebrafish larva\|strain:mixed\|age:7 dpf loc name:missing\|collection date:missing	zebrafish larva neurons and glia scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish larva	About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neurons and glia\|tissue:zebrafish larva\|strain:mixed\|age:7 dpf	GSM7720759	GSM7720759: zebrafish larva neurons and glia scRNAseq; Danio rerio; RNA Seq	GSM7720759 r1	GSM7720759	1	About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing 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	SRP456253		loader:fastq load.py	CEL210928PB_HW1008_SAIG_D7_S1_L002_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L002_R2_001.fastq.gz	fastq fastq fastq fastq	55936355640.0	254256162.0	GSM7720759 r1	0:10 1:10 2:100 3:100	A:13207297968;C:10496996981;G:10989402500;T:16156355819;N:1179132	10	10	100	100	13207297968	10496996981	10989402500	16156355819	1179132	SRX21445937	SRS18680715	SRA1696793	Oregon Health and Science Univ	Oregon Health and Science Univ	2	0.0	0.81961	0.0	0.19165	1.0	0.8508		0.59575	100	100	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-21	Larval	Larval	Multi-tissue	Multi-system
25238	25238	SRR25721802	SRX21445937	SRS18680715	SRP456253	PRJNA1007646	Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival [larva]	GSE241296	Other	Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach we demonstrate that larval RBs in zebrafish fall into three largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib which is used in clinic and causes peripheral neuropathy. Importantly dovitinib mediated axon loss can be suppressed by loss of Sarm1 a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration…				zebrafish larva neurons and glia scRNAseq	GSM7720759		source name:zebrafish larva\|cell type:neurons and glia\|tissue:zebrafish larva\|strain:mixed\|age:7 dpf loc name:missing\|collection date:missing	zebrafish larva neurons and glia scRNAseq	using Cell Ranger version 3.1.0; 10X Genomics Pleasanton CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files	zebrafish larva	About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol 10x Genomics.		cell type:neurons and glia\|tissue:zebrafish larva\|strain:mixed\|age:7 dpf	GSM7720759	GSM7720759: zebrafish larva neurons and glia scRNAseq; Danio rerio; RNA Seq	GSM7720759 r1	GSM7720759	1	About 150 dpf 7 dpf larva were euthanized in 0.02% tricaine and individually decapitated behind the hindbrain. They were incubated with 20 mg/ml collagenase Life Sciences in a buffer containing 134 mM NaCl 2.9 mM KCl 1.2 mM MgCl2 2.1 mM CaCl2 and 10 mM Na HEPES pH 7.8 at 28 °C for 2 hr with intermittent trituration using a p200 pipette aid at 0 0.5 hr and 1 hr of the incubation. To release spinal cords from remaining tissue the final triturations were done using fire polished Pasteur pipettes with decreased opening sizes 300 200 100 μm respectively. Intact spinal cords were transferred to L15 media and washed 3 times with fresh media. The spinal cords were incubated with 0.25% trypsin solution in 1xPBS containing 1 mM EDTA at 28 °C for 25 min. The digestion was terminated by adding 500 μl stop solution L15 with 1% fetal bovine serum. The tissue was collected by spinning at 400 g for 3 min at 4°C washed once with L15 and resuspended in 200 μl of L15 media. Spinal cord cells were dissociated by triturating the digested tissue with fire polished Pasteur pipettes with 80 100 μm opening. The solution was filtered through a 35 μm strainer into a siliconized collection tube. The suspension was examined on a microscope for cell count Trypan blue staining based viability test and proportion of dispersed single cells. Samples with a viability above 70% were used for sequencing 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	SRP456253		loader:fastq load.py	CEL210928PB_HW1008_SAIG_D7_S1_L001_I1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_I2_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R1_001.fastq.gz CEL210928PB_HW1008_SAIG_D7_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	54474841080.0	247612914.0	GSM7720759 r2	0:10 1:10 2:100 3:100	A:12887048507;C:10210716068;G:10683375130;T:15740176261;N:1266834	10	10	100	100	12887048507	10210716068	10683375130	15740176261	1266834	SRX21445937	SRS18680715	SRA1696793	Oregon Health and Science Univ	Oregon Health and Science Univ	2	0.0	0.82189	0.0	0.19349	1.0	0.85025		0.6092	100	100	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-21	Larval	Larval	Multi-tissue	Multi-system
26482	26482	SRR25930974	SRX21649989	SRS18818461	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		80hpf	GSM7764482		source name:heart\|tissue:heart\|genotype:wild type\|age:80hpf\|geo loc name:missing\|collection date:missing	80hpf	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:80hpf	GSM7764482	GSM7764482: 80hpf; Danio rerio; RNA Seq	GSM7764482 r1	GSM7764482	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_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz	fastq fastq	18811433188.0	225273324.0	GSM7764482 r1	0:28 1:55.50	A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878	28	55			5135587480	4020079745	4129712330	5427444755	98608878	SRX21649989	SRS18818461	SRA1706674	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	2	0.00187	0.93611	0.00071	0.16105	0.99626	0.79825	0.41545	0.50249	28	55	T	B	sc-like readlen	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2023-09-06	Larval	Larval	Heart	Cardiovascular System
28771	28771	SRR26639098	SRX22339478	SRS19389127	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 2 snRNAseq	GSM7880035		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880035	GSM7880035: sibling replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880035 r1	GSM7880035	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_2_S1_L001_R1_001.fastq.gz sib_2_S1_L001_R2_001.fastq.gz	fastq fastq	29585942468.0	250728326.0	GSM7880035 r1	0:29 1:89	A:8869085825;C:6519678188;G:6681924988;T:7515095066;N:158401	29	89			8869085825	6519678188	6681924988	7515095066	158401	SRX22339478	SRS19389127	SRA1744308	University of Bern	University of Bern	2	0.03708	0.89742	0.02638	0.33817	0.98766	0.87265	0.50529	0.84547	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28772	28772	SRR26639099	SRX22339478	SRS19389127	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 2 snRNAseq	GSM7880035		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880035	GSM7880035: sibling replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880035 r1	GSM7880035	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz	fastq fastq	29238445684.0	247783438.0	GSM7880035 r2	0:29 1:89	A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758	29	89			8764474921	6441070570	6601843083	7430828352	228758	SRX22339478	SRS19389127	SRA1744308	University of Bern	University of Bern	2	0.03758	0.89628	0.02664	0.33912	0.98711	0.87442	0.4887	0.42456	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28773	28773	SRR26639100	SRX22339477	SRS19389126	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 1 snRNAseq	GSM7880034		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880034	GSM7880034: sibling replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880034 r1	GSM7880034	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_1_S1_L001_R1_001.fastq.gz sib_1_S1_L001_R2_001.fastq.gz	fastq fastq	24652163520.0	208916640.0	GSM7880034 r1	0:29 1:89	A:7206225437;C:5487875216;G:5870141423;T:6087790451;N:130993	29	89			7206225437	5487875216	5870141423	6087790451	130993	SRX22339477	SRS19389126	SRA1744308	University of Bern	University of Bern	2	0.04136	0.8662	0.02868	0.3899	0.98597	0.86906	0.42284	0.79265	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28774	28774	SRR26639101	SRX22339477	SRS19389126	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 1 snRNAseq	GSM7880034		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880034	GSM7880034: sibling replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880034 r1	GSM7880034	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_1_S1_L002_R1_001.fastq.gz sib_1_S1_L002_R2_001.fastq.gz	fastq fastq	24333156656.0	206213192.0	GSM7880034 r2	0:29 1:89	A:7112369699;C:5414867956;G:5792728480;T:6013000607;N:189914	29	89			7112369699	5414867956	5792728480	6013000607	189914	SRX22339477	SRS19389126	SRA1744308	University of Bern	University of Bern	2	0.04141	0.86578	0.02866	0.39157	0.98614	0.8704	0.42701	0.78792	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28775	28775	SRR26639102	SRX22339476	SRS19389125	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 2 snRNAseq	GSM7880033		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880033	GSM7880033: spns mutant replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880033 r1	GSM7880033	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_2_S1_L001_R1_001.fastq.gz mut_2_S1_L001_R2_001.fastq.gz	fastq fastq	33067082062.0	280229509.0	GSM7880033 r1	0:29 1:89	A:9837791085;C:7302189072;G:7479072379;T:8447851569;N:177957	29	89			9837791085	7302189072	7479072379	8447851569	177957	SRX22339476	SRS19389125	SRA1744308	University of Bern	University of Bern	2	0.03975	0.89392	0.02827	0.35098	0.98693	0.87572	0.42665	0.8308	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28776	28776	SRR26639103	SRX22339476	SRS19389125	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 2 snRNAseq	GSM7880033		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880033	GSM7880033: spns mutant replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880033 r1	GSM7880033	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_2_S1_L002_R1_001.fastq.gz mut_2_S1_L002_R2_001.fastq.gz	fastq fastq	32794778418.0	277921851.0	GSM7880033 r2	0:29 1:89	A:9757463504;C:7238976466;G:7415128557;T:8382951671;N:258220	29	89			9757463504	7238976466	7415128557	8382951671	258220	SRX22339476	SRS19389125	SRA1744308	University of Bern	University of Bern	2	0.04055	0.89543	0.02892	0.35129	0.98654	0.87655	0.45394	0.85056	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28777	28777	SRR26639104	SRX22339475	SRS19389124	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 1 snRNAseq	GSM7880032		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880032	GSM7880032: spns mutant replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880032 r1	GSM7880032	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz	fastq fastq	30027997254.0	254474553.0	GSM7880032 r1	0:29 1:89	A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572	29	89			9128230353	6473885422	6895366272	7530354635	160572	SRX22339475	SRS19389124	SRA1744308	University of Bern	University of Bern	2	0.03908	0.86231	0.0274	0.38263	0.98701	0.87113	0.48114	0.78783	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28778	28778	SRR26639105	SRX22339475	SRS19389124	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 1 snRNAseq	GSM7880032		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880032	GSM7880032: spns mutant replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880032 r1	GSM7880032	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_1_S1_L002_R1_001.fastq.gz mut_1_S1_L002_R2_001.fastq.gz	fastq fastq	29506651188.0	250056366.0	GSM7880032 r2	0:29 1:89	A:8967217701;C:6359649244;G:6775979696;T:7403576105;N:228442	29	89			8967217701	6359649244	6775979696	7403576105	228442	SRX22339475	SRS19389124	SRA1744308	University of Bern	University of Bern	2	0.03885	0.86188	0.02749	0.38666	0.98644	0.86975	0.46306	0.79451	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
29174	29174	SRR27237224	SRX22915658	SRS19883761	SRP478464	PRJNA1053781	Single cell gene expression profie of developing photoreceptor cells in larval zebrafish	GSE250379	Other	Molecular underpinnings of vertebrate retinal differentiation and maturation are poorly understood particularly for non mammalian species. We generated single cell transcriptome data from the larval zebrafish retina and characterized gene expression diversity among photoreceptor subtypes and their progenitors. Overall design: GFP positive differentiating photoreceptor cells and bipolar cells were collected from 4 dpf larval transgenic zebrafish Tgcrx:EGFPstl887 using fluorescence activated cell sorting.	parent bioproject:PRJNA1050288	pubmed:39531499		retina scRNA seq	GSM7978132		source name:retina\|tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf\|geo loc name:missing\|collection date:missing	retina scRNA seq	Read alignment and initial quality control were performed using Cell Ranger software version 7.0.0 10X Genomics. Assembly: GRCz11 Supplementary files format and content: Tab separated value file and matrix file	retina	Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks’ Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.		tissue:retina\|genotype:Tgcrx:EGFPstl887\|developmental stage:4 dpf	GSM7978132	GSM7978132: retina scRNA seq; Danio rerio; RNA Seq	GSM7978132 r1	GSM7978132	1	Fifty heads were dissected from 4 dpf heterozygous Tgcrx:GFPstl887Tg larvae. Following dissection eyes were stored in ice cold Hanks' Balanced Salt Solution HBSS until all eyes were harvested. Once the eyes were collected HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium free HBSS containing 0.4 mg papain Worthington Biochem for 15 min at 37°C. 800 µl of 10% fetal bovine serum FBS in Dulbecco's Modified Eagle Medium DMEM containing 5mM MgCl2 and 120 units DNaseI Roche were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer 2.5 mM EDTA 25 mM HEPES 1% bovine serum albumin BSA in calcium/magnesium free HBSS. Cells were sorted on an Aria II FACS machine BD biosciences with gating based on forward scatter side scatter and GFP fluorescence and collected in 700 μl of D PBS without xxx+ and Mg2+ supplemented with 0.4 % BSA D PBS CMF in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min washed with D PBS CMF centrifuged and supernatant reduced to 80 µl. Cell density was quantified on a hemocytometer and 5000 cells were used for single cell library preparation. A library for single cell RNA seq was constructed with the Chromium v3 platform 10X Genomics Pleasanton CA according to the manufacturer protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP478464		loader:fastq load.py	crx.crx_S1_L003_R1_001.fastq.gz crx.crx_S1_L003_R2_001.fastq.gz	fastq fastq	45170138494.0	253764823.0	GSM7978132 r1	0:28 1:150	A:13826023801;C:9023674621;G:9590649474;T:12728940802;N:849796	28	150			13826023801	9023674621	9590649474	12728940802	849796	SRX22915658	SRS19883761	SRA1770358	Pathology and Immunology, Washington University School of Medicine	Pathology and Immunology, Washington University School of Medicine	2	0.0046	0.87155	0.00206	0.2263	0.99168	0.77784	0.30223	0.50112	28	150	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-12-17	Larval	Larval	Eye	Sensory System
29187	29187	SRR8176747	SRX4996876	SRS4031879	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf		pubmed:38529407		Nadia 19dpf ZZ Gonad Single Cell RNA Seq	Nadia 19dpf ZZ Gonad Single Cell RNA Seq		strain:Nadia\|age:19 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZZ\|BioSampleModel:Model organism or animal								scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad	Nadia 19dpf ZZ gonad	Nadia 19dpf ZZ gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945		loader:fastq load.py			15090036999.0	107021539.0	zz 19NAmale I1 001.fastq.gz	0:8 1:133	A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127	8	133			4154103253	3402890354	3765557416	3755723849	11762127	SRX4996876	SRS4031879	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Larval	Larval	Gonad	Reproductive System
29190	29190	SRR8176756	SRX4996867	SRS4031876	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf		pubmed:38529407		Nadia 19dpf ZW Gonad Single Cell RNA Seq	Nadia 19dpf ZW Gonad Single Cell RNA Seq		strain:Nadia\|age:19 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZW\|BioSampleModel:Model organism or animal								scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad	Nadia 19dpf ZW gonad	Nadia 19dpf ZW gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945		loader:fastq load.py			17141425554.0	121570394.0	zw 19NAfem I1 001.fastq.gz	0:8 1:133	A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745	8	133			4656207219	3824531650	4322736498	4324676442	13273745	SRX4996867	SRS4031876	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Larval	Larval	Gonad	Reproductive System
30692	30692	SRR29655998	SRX25159999	SRS21850513	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC145382 HuNoV infected replicate 1 scRNAseq	GSM8370069		tissue:Tg mpeg:mCherry\|cell line:Tg mpeg:mCherry\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC145382 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger	Tg mpeg:mCherry	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		cell line:Tg mpeg:mCherry\|cell type:120 hpf\|infection:HuNoV infected	GSM8370069	GSM8370069: GC145382 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8370069 r1	GSM8370069	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC145382_SI-GA-B1_S1_L001_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L001_R2_001.fastq.gz	fastq fastq	5781664526.0	48997157.0	GSM8370069 r1	0:28 1:90	A:1659071356;C:1268706433;G:1342749232;T:1510681009;N:456496	28	90			1659071356	1268706433	1342749232	1510681009	456496	SRX25159999	SRS21850513	SRA1913292	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-06-30	Larval	Larval	Cell Line	Cell Line
30693	30693	SRR29655999	SRX25159999	SRS21850513	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC145382 HuNoV infected replicate 1 scRNAseq	GSM8370069		tissue:Tg mpeg:mCherry\|cell line:Tg mpeg:mCherry\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC145382 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger	Tg mpeg:mCherry	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		cell line:Tg mpeg:mCherry\|cell type:120 hpf\|infection:HuNoV infected	GSM8370069	GSM8370069: GC145382 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8370069 r1	GSM8370069	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC145382_SI-GA-B1_S1_L002_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L002_R2_001.fastq.gz	fastq fastq	6046508328.0	51241596.0	GSM8370069 r2	0:28 1:90	A:1731027394;C:1330440539;G:1408717533;T:1575870623;N:452239	28	90			1731027394	1330440539	1408717533	1575870623	452239	SRX25159999	SRS21850513	SRA1913292	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-06-30	Larval	Larval	Cell Line	Cell Line
30694	30694	SRR28272066	SRX23882001	SRS20705714	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122775 HuNoV infected replicate 2 scRNAseq	GSM8136771		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122775 HuNoV infected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136771	GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136771 r1	GSM8136771	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz	fastq fastq	6487168261.0	54514019.0	GSM8136771 r1	0:28 1:91	A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286	28	91			1754199332	1533792234	1687916105	1511168304	92286	SRX23882001	SRS20705714	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30695	30695	SRR28272067	SRX23882001	SRS20705714	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122775 HuNoV infected replicate 2 scRNAseq	GSM8136771		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122775 HuNoV infected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136771	GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136771 r1	GSM8136771	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz	fastq fastq	6313572727.0	53055233.0	GSM8136771 r2	0:28 1:91	A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282	28	91			1709609257	1491468410	1640296277	1472111501	87282	SRX23882001	SRS20705714	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30696	30696	SRR28272068	SRX23882000	SRS20705713	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122774 HuNoV infected replicate 1 scRNAseq	GSM8136770		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122774 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136770	GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136770 r1	GSM8136770	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz	fastq fastq	15738518978.0	132256462.0	GSM8136770 r1	0:28 1:91	A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212	28	91			4181691582	3761213961	4083789142	3711597081	227212	SRX23882000	SRS20705713	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30697	30697	SRR28272069	SRX23882000	SRS20705713	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122774 HuNoV infected replicate 1 scRNAseq	GSM8136770		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected\|geo loc name:missing\|collection date:missing	GC122774 HuNoV infected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:HuNoV infected	GSM8136770	GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136770 r1	GSM8136770	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz	fastq fastq	15261653253.0	128249187.0	GSM8136770 r2	0:28 1:91	A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693	28	91			4059552936	3644406570	3954261902	3603216152	215693	SRX23882000	SRS20705713	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30698	30698	SRR28272070	SRX23881999	SRS20705712	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122773 uninfected replicate 2 scRNAseq	GSM8136769		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122773 uninfected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136769	GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136769 r1	GSM8136769	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz	fastq fastq	15150656598.0	127316442.0	GSM8136769 r1	0:28 1:91	A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113	28	91			4100783574	3526779401	3845684506	3677189004	220113	SRX23881999	SRS20705712	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30699	30699	SRR28272071	SRX23881999	SRS20705712	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122773 uninfected replicate 2 scRNAseq	GSM8136769		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122773 uninfected replicate 2 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136769	GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq	GSM8136769 r1	GSM8136769	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz	fastq fastq	14942015326.0	125563154.0	GSM8136769 r2	0:28 1:91	A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808	28	91			4048600218	3475105088	3787275869	3630822343	211808	SRX23881999	SRS20705712	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30700	30700	SRR28272072	SRX23881998	SRS20705711	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122772 uninfected replicate 1 scRNAseq	GSM8136768		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122772 uninfected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136768	GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136768 r1	GSM8136768	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz	fastq fastq	7397061301.0	62160179.0	GSM8136768 r1	0:28 1:91	A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806	28	91			2023651844	1711760729	1860691426	1800850496	106806	SRX23881998	SRS20705711	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30701	30701	SRR28272073	SRX23881998	SRS20705711	SRP494129	PRJNA1085664	Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile	GSE261163	Transcriptome Analysis	Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.		pubmed:39584740		GC122772 uninfected replicate 1 scRNAseq	GSM8136768		source name:Intestines\|tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected\|geo loc name:missing\|collection date:missing	GC122772 uninfected replicate 1 scRNAseq	Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger	Intestines	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.		tissue:Intestines\|cell line:wildtype AB\|cell type:120 hpf\|infection:uninfected	GSM8136768	GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq	GSM8136768 r1	GSM8136768	1	Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494129			GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz	fastq fastq	7290496444.0	61264676.0	GSM8136768 r2	0:28 1:91	A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196	28	91			1996736343	1685693360	1830823892	1777138653	104196	SRX23881998	SRS20705711	SRA1820104	Genomics Core Leuven	Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute												T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-03-08	Larval	Larval	Gut	Digestive System
30775	30775	SRR28357669	SRX23962905	SRS20762620	SRP495490	PRJNA1088483	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA Seq]	GSE261718	Other	Purpose: To explore the endogenous expression pattern of Erbb2. Methods: Approximately 1000 hearts dissected from 72 hpf Tgmyl7:mCherry embryos were digested in 0.25% trypsin EDTA solution for single cell RNA sequencing. Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2 but weakly expressed in subcluster 3 10 and 12. Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation. Overall design: 72 hpf Tgmyl7:mCherry zebrafish hearts were collected for single cell RNA sequencing.		pubmed:40053597		S72hpf trunks	GSM8149579		source name:zebrafish hearts\|tissue:zebrafish hearts\|cell line:Tgmyl7:mCherry heart cells\|cell type:zebrafish heart cells\|geo loc name:missing\|collection date:missing	S72hpf trunks	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: zip compressed files include filtered gene bc matrices post running CellRanger pipeline	zebrafish hearts	A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer’s instructions. Single cell RNA Seq 10x	Dechorionated zebrafish embryos were maintained in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h light/dark.	tissue:zebrafish hearts\|cell line:Tgmyl7:mCherry heart cells\|cell type:zebrafish heart cells	GSM8149579	GSM8149579: S72hpf trunks; Danio rerio; RNA Seq	GSM8149579 r1	GSM8149579	1	A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer's instructions. Single cell RNA Seq 10x		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495490			zebrafish_heart_72h_R1_fastq.gz zebrafish_heart_72h_R2_fastq.gz	fastq fastq	155978889600.0	519929632.0	GSM8149579 r1	0:150 1:150	A:63302225780;C:28042347630;G:26792086978;T:37838422350;N:3806862	150	150			63302225780	28042347630	26792086978	37838422350	3806862	SRX23962905	SRS20762620	SRA1825277	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.0	0.92044	0.0	0.11022	1.0	0.80996		0.54499	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-03-15	Larval	Larval	Heart	Cardiovascular System
31525	31525	SRR28419473	SRX24023800	SRS20818155	SRP497235	PRJNA1090867	Single cell RNA seq of zebrafish endothelial cells	GSE262232	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.		pubmed:39977018		Zebrafish endothelial cells 3 dpf 2	GSM8160887		source name:Whole body\|tissue:Whole body\|age:embryo\|geo loc name:missing\|collection date:missing	Zebrafish endothelial cells 3 dpf 2	Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files perform the alignment barcode counting and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files	Whole body	Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.		tissue:Whole body\|age:embryo	GSM8160887	GSM8160887: Zebrafish endothelial cells 3 dpf 2; Danio rerio; RNA Seq	GSM8160887 r1	GSM8160887	1	Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP497235		assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped\|dangling references:skip reference resolution	3dpf_2_possorted_genome_bam.bam	10X Genomics bam file	8478190406.0	86512147.0	GSM8160887 r1	0:98	A:2448546566;C:1819820402;G:2005413327;T:2187171703;N:17238408	98				2448546566	1819820402	2005413327	2187171703	17238408	SRX24023800	SRS20818155	SRA1835509	Uppsala University	Uppsala University	1	0.91631		0.11199		0.82106		0.54746		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-03-22	Larval	Larval	Trunk	Surface Structure
31526	31526	SRR28419474	SRX24023799	SRS20818156	SRP497235	PRJNA1090867	Single cell RNA seq of zebrafish endothelial cells	GSE262232	Transcriptome Analysis	We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.		pubmed:39977018		Zebrafish endothelial cells 3 dpf 1	GSM8160886		source name:Whole body\|tissue:Whole body\|age:embryo\|geo loc name:missing\|collection date:missing	Zebrafish endothelial cells 3 dpf 1	Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files perform the alignment barcode counting and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files	Whole body	Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.		tissue:Whole body\|age:embryo	GSM8160886	GSM8160886: Zebrafish endothelial cells 3 dpf 1; Danio rerio; RNA Seq	GSM8160886 r1	GSM8160886	1	Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 1500	SRP497235		assembly:GRCz11\|intentional duplicate\|dangling references:treat as unmapped\|dangling references:skip reference resolution	3dpf_1_possorted_genome_bam.bam	10X Genomics bam file	2842123088.0	29001256.0	GSM8160886 r1	0:98	A:821846800;C:603425858;G:657525459;T:720690292;N:38634679	98				821846800	603425858	657525459	720690292	38634679	SRX24023799	SRS20818156	SRA1835509	Uppsala University	Uppsala University	1	0.86292		0.0954		0.82844		0.52761		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Sweden	2024-03-22	Larval	Larval	Trunk	Surface Structure
31855	31855	SRR28735563	SRX24301542	SRS21065461	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 2 scRNASeq	GSM8215882		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215882	GSM8215882: stim2KO repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215882 r1	GSM8215882	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0006_P24_V11_S5_R2_001.fastq.gz RIS_F63_0006_P24_V11_S5_R1_001.fastq.gz	fastq fastq	18259545984.0	142652703.0	GSM8215882 r1	0:28 1:100	A:5244714575;C:3875508560;G:4200332154;T:4938304565;N:686130	28	100			5244714575	3875508560	4200332154	4938304565	686130	SRX24301542	SRS21065461	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.0154	0.87839	0.00603	0.34485	0.99011	0.78403	0.22547	0.56166	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31856	31856	SRR28735564	SRX24301542	SRS21065461	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 2 scRNASeq	GSM8215882		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215882	GSM8215882: stim2KO repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215882 r1	GSM8215882	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0006_P24_V12_S6_R2_001.fastq.gz RIS_F63_0006_P24_V12_S6_R1_001.fastq.gz	fastq fastq	17876561664.0	139660638.0	GSM8215882 r2	0:28 1:100	A:5103195386;C:3808218494;G:4122439805;T:4842033472;N:674507	28	100			5103195386	3808218494	4122439805	4842033472	674507	SRX24301542	SRS21065461	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01605	0.88209	0.00613	0.34048	0.99005	0.78569	0.24462	0.56679	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31857	31857	SRR28735565	SRX24301542	SRS21065461	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 2 scRNASeq	GSM8215882		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215882	GSM8215882: stim2KO repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215882 r1	GSM8215882	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0006_P24_V13_S7_R2_001.fastq.gz RIS_F63_0006_P24_V13_S7_R1_001.fastq.gz	fastq fastq	11789486464.0	92105363.0	GSM8215882 r3	0:28 1:100	A:3373601519;C:2511268571;G:2715549864;T:3188625976;N:440534	28	100			3373601519	2511268571	2715549864	3188625976	440534	SRX24301542	SRS21065461	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01608	0.87817	0.00612	0.34136	0.98979	0.78626	0.23961	0.56904	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31858	31858	SRR28735566	SRX24301542	SRS21065461	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 2 scRNASeq	GSM8215882		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215882	GSM8215882: stim2KO repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215882 r1	GSM8215882	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0006_P24_V14_S8_R2_001.fastq.gz RIS_F63_0006_P24_V14_S8_R1_001.fastq.gz	fastq fastq	15492682752.0	121036584.0	GSM8215882 r4	0:28 1:100	A:4403489633;C:3300131260;G:3589771700;T:4198706550;N:583609	28	100			4403489633	3300131260	3589771700	4198706550	583609	SRX24301542	SRS21065461	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.0161	0.88184	0.0062	0.34153	0.99072	0.78593	0.23108	0.5637	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31859	31859	SRR28735567	SRX24301541	SRS21065460	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 scRNASeq	GSM8215881		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215881	GSM8215881: stim2KO repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215881 r1	GSM8215881	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0005_P24_V11_S1_R2_001.fastq.gz RIS_F63_0005_P24_V11_S1_R1_001.fastq.gz	fastq fastq	19966585728.0	155988951.0	GSM8215881 r1	0:28 1:100	A:5812540331;C:4168323325;G:4507287467;T:5477684057;N:750548	28	100			5812540331	4168323325	4507287467	5477684057	750548	SRX24301541	SRS21065460	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01363	0.87301	0.00566	0.36217	0.99046	0.78224	0.23254	0.57232	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31860	31860	SRR28735568	SRX24301541	SRS21065460	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 scRNASeq	GSM8215881		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215881	GSM8215881: stim2KO repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215881 r1	GSM8215881	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0005_P24_V12_S2_R2_001.fastq.gz RIS_F63_0005_P24_V12_S2_R1_001.fastq.gz	fastq fastq	17678874240.0	138116205.0	GSM8215881 r2	0:28 1:100	A:5142406165;C:3696946044;G:3986515668;T:4852338487;N:667876	28	100			5142406165	3696946044	3986515668	4852338487	667876	SRX24301541	SRS21065460	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01372	0.87988	0.00546	0.35939	0.99082	0.78042	0.23783	0.55977	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31861	31861	SRR28735569	SRX24301541	SRS21065460	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 scRNASeq	GSM8215881		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215881	GSM8215881: stim2KO repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215881 r1	GSM8215881	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0005_P24_V13_S3_R2_001.fastq.gz RIS_F63_0005_P24_V13_S3_R1_001.fastq.gz	fastq fastq	13000627968.0	101567406.0	GSM8215881 r3	0:28 1:100	A:3777994303;C:2720540507;G:2933782069;T:3567821225;N:489864	28	100			3777994303	2720540507	2933782069	3567821225	489864	SRX24301541	SRS21065460	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01334	0.87202	0.0054	0.35922	0.98987	0.78173	0.25273	0.56267	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31862	31862	SRR28735570	SRX24301541	SRS21065460	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		stim2KO repllicate 1 scRNASeq	GSM8215881		source name:head\|tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	stim2KO repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:stim2a;stim2b / ; TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215881	GSM8215881: stim2KO repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215881 r1	GSM8215881	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0005_P24_V14_S4_R2_001.fastq.gz RIS_F63_0005_P24_V14_S4_R1_001.fastq.gz	fastq fastq	12242602112.0	95645329.0	GSM8215881 r4	0:28 1:100	A:3556852182;C:2559826440;G:2764616604;T:3360845193;N:461693	28	100			3556852182	2559826440	2764616604	3360845193	461693	SRX24301541	SRS21065460	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.014	0.87833	0.00561	0.35801	0.98991	0.78299	0.25702	0.57284	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31863	31863	SRR28735571	SRX24301540	SRS21065458	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 2 scRNASeq	GSM8215880		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215880	GSM8215880: Tg repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215880 r1	GSM8215880	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0008_P24_V11_S13_R1_001.fastq.gz RIS_F63_0008_P24_V11_S13_R2_001.fastq.gz	fastq fastq	18512923264.0	144632213.0	GSM8215880 r1	0:28 1:100	A:5256155736;C:3979781355;G:4312684581;T:4963605318;N:696274	28	100			5256155736	3979781355	4312684581	4963605318	696274	SRX24301540	SRS21065458	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01316	0.89227	0.00508	0.28873	0.98879	0.78218	0.25886	0.54866	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31864	31864	SRR28735572	SRX24301540	SRS21065458	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 2 scRNASeq	GSM8215880		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215880	GSM8215880: Tg repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215880 r1	GSM8215880	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0008_P24_V12_S14_R1_001.fastq.gz RIS_F63_0008_P24_V12_S14_R2_001.fastq.gz	fastq fastq	17486730368.0	136615081.0	GSM8215880 r2	0:28 1:100	A:4977460950;C:3751371688;G:4054389958;T:4702849436;N:658336	28	100			4977460950	3751371688	4054389958	4702849436	658336	SRX24301540	SRS21065458	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01383	0.89285	0.00539	0.29088	0.98869	0.78171	0.23958	0.53551	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31865	31865	SRR28735573	SRX24301540	SRS21065458	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 2 scRNASeq	GSM8215880		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215880	GSM8215880: Tg repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215880 r1	GSM8215880	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0008_P24_V13_S15_R2_001.fastq.gz RIS_F63_0008_P24_V13_S15_R1_001.fastq.gz	fastq fastq	12906420736.0	100831412.0	GSM8215880 r3	0:28 1:100	A:3667742915;C:2775193040;G:3000852761;T:3462146052;N:485968	28	100			3667742915	2775193040	3000852761	3462146052	485968	SRX24301540	SRS21065458	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01323	0.8936	0.00513	0.28955	0.98859	0.7807	0.22054	0.54431	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31866	31866	SRR28735574	SRX24301540	SRS21065458	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 2 scRNASeq	GSM8215880		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 2 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215880	GSM8215880: Tg repllicate 2 scRNASeq; Danio rerio; RNA Seq	GSM8215880 r1	GSM8215880	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0008_P24_V14_S16_R1_001.fastq.gz RIS_F63_0008_P24_V14_S16_R2_001.fastq.gz	fastq fastq	13809295616.0	107885122.0	GSM8215880 r4	0:28 1:100	A:3926766598;C:2968211018;G:3214515151;T:3699280941;N:521908	28	100			3926766598	2968211018	3214515151	3699280941	521908	SRX24301540	SRS21065458	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.013	0.89441	0.00484	0.28706	0.98912	0.78027	0.25093	0.54201	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31867	31867	SRR28735575	SRX24301539	SRS21065459	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 1 scRNASeq	GSM8215879		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215879	GSM8215879: Tg repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215879 r1	GSM8215879	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0007_P24_V11_S9_R2_001.fastq.gz RIS_F63_0007_P24_V11_S9_R1_001.fastq.gz	fastq fastq	25846470784.0	201925553.0	GSM8215879 r1	0:28 1:100	A:7418557669;C:5494387747;G:5909175364;T:7023377435;N:972569	28	100			7418557669	5494387747	5909175364	7023377435	972569	SRX24301539	SRS21065459	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01293	0.89145	0.00523	0.30321	0.98914	0.77733	0.2598	0.55188	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31868	31868	SRR28735576	SRX24301539	SRS21065459	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 1 scRNASeq	GSM8215879		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215879	GSM8215879: Tg repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215879 r1	GSM8215879	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0007_P24_V12_S10_R2_001.fastq.gz RIS_F63_0007_P24_V12_S10_R1_001.fastq.gz	fastq fastq	21735339264.0	169807338.0	GSM8215879 r2	0:28 1:100	A:6224752343;C:4637507813;G:4990390025;T:5881869873;N:819210	28	100			6224752343	4637507813	4990390025	5881869873	819210	SRX24301539	SRS21065459	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.0129	0.89405	0.00501	0.30007	0.9892	0.77865	0.25727	0.55148	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31869	31869	SRR28735577	SRX24301539	SRS21065459	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 1 scRNASeq	GSM8215879		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215879	GSM8215879: Tg repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215879 r1	GSM8215879	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0007_P24_V13_S11_R1_001.fastq.gz RIS_F63_0007_P24_V13_S11_R2_001.fastq.gz	fastq fastq	143588480.0	1121785.0	GSM8215879 r3	0:28 1:100	A:41267450;C:30625679;G:32896572;T:38793424;N:5355	28	100			41267450	30625679	32896572	38793424	5355	SRX24301539	SRS21065459	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01306	0.89063	0.00499	0.29993	0.98898	0.78084	0.26395	0.55218	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31870	31870	SRR28735578	SRX24301539	SRS21065459	SRP502616	PRJNA1101946	Loss of Stim2 in zebrafish induces retinal gene expression cellular changes resembling glaucoma characteristics [scRNA seq]	GSE264310	Transcriptome Analysis	Calcium is involved in vision processes in retina and is implicated in various pathologies including glaucoma. Rods are protected against prolonged lowering of intracellular calcium ion concentrations by Store Operated Calcium Entry SOCE. We showed zebrafish lacking SOCE calcium sensor Stim2 had problem with vision as indicated by behavior tests staining of retina and downregulation of genes related to light perception. In this work we aimed to understand the mechanism responsible for the vision problems in stim2 zebrafish knockout. scRNA sequencing of neuronal origin cells from brains of 5 dpf larvae identified 27 clusters. Differently expressed genes were detected in ten clusters including amacrine and GABAergic retinal interneurons and GABAergic optic tectum cells. In five clusters the proportion of cells in stim2 KO fish versus control was significantly decreased including GABAergic diencephalon and optic tectum and was increased in amacrine and GABAergic retinal interneurons. Transmission Electron Microscopy in stim2 KO fish revealed decrease in width of inner plexiform layer IPL ganglion cells and their dendrites numbers what is characteristic for glaucoma. Analysis of cell density in the inner nucleus layer which includes amacrine cells among others showed a significant decrease in the number of GABAergic neurons.The area of cristae in photoreceptor mitochondria was statistically lower in stim2 KO than in control retinas. Overall design: TgHuC:GCaMP5G zebrafish line and double knockout for stim2 expressing GCaMP5G under the same promoter [stim2a;stim2b / ; TgHuC:GCaMP5G] were used. Single cell suspensions were obtained by enzymatic and mechanical digestion of 5 dpf dpf larva heads without xxx isolated from two fish lines: stim2 KO 2 replicates 30 larvae per each sample and Tg control 2 replicates 30 larvae per each sample. The cells were sorted based on GCaMP5G fluorescence to obtain the cells of neuronal origin.	parent bioproject:PRJNA1101942	pubmed:39424970		Tg repllicate 1 scRNASeq	GSM8215879		source name:head\|tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae\|geo loc name:missing\|collection date:missing	Tg repllicate 1 scRNASeq	Raw reads from fastq files were mapped to the zebrafish reference genome GRCz11 and gene expression were quantified with STARSolo mode of STAR for each sample with the following parameters: soloType CB UMI Simple soloCBwhitelist 3M february 2018.txt [from Cell Ranger] soloUMIlen 12 soloCBmatchWLtype 1MM multi Nbase pseudocounts soloUMIfiltering MultiGeneUMI CR soloUMIdedup 1MM CR soloCellFilter EmptyDrops CR Assembly: Danio rerio GRCz11 Supplementary files format and content: Tab separated values files and matrix files	head	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit’s standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer’s protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual’s guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		tissue:head\|cell type:neuronal\|genotype:TgHuC:GCaMP5G\|age:5 dpf larvae	GSM8215879	GSM8215879: Tg repllicate 1 scRNASeq; Danio rerio; RNA Seq	GSM8215879 r1	GSM8215879	1	5 dpf larvae were anesthetized by tricaine methanesulfonate MS222 a neuromuscular blocker and heads were dissected in Dulbecco's Modified Eagle Medium/Nutrient Mixture F 12 DMEM/F 12; with Ca2+ and L glutamine and without xxx and Phenol Red; Gibco with 10% fetal bovine serum FBS; Gibco. Eyes were surgically removed from the fish to focus on the cells of neuronal origins. Single cell suspensions were obtained by enzymatic and mechanical digestion of heads without xxx isolated from two fish lines: stim2 KO and Tg control. Immediately post isolation of single cell suspension the cells were sorted based on GCaMP5G fluorescence with 488 nm excitation and 510 nm emission to obtain the cells of neuronal origin. The GCaMP5 was expressed under the elav/Huc promoter which is an early marker of neuronal cells. Cell sorting was performed with a BD FACSAria II BD Biosciences Franklin Lakes NJ. Cell viability was measured using the trypan blue staining method and when the viability of cells was 80% the cells were immediately loaded on the 10X Chromium system for droplet encapsulation. Approximately 8000 cells were sorted and suspended in 40 μl volume. Cells were loaded according to the Chromium single cell 3′ kit's standard protocol V3 chemistry. To prepare the cells for droplet based sequencing GCaMP5G positive single cell suspension was carefully mixed with reverse transcription mix before loading the cells on the 10X Genomics Chromium system the standard manufacturer's protocol. During the encapsulation the cells were lysed within the droplet and they released polyadenylated RNA bound to the barcoded bead which was encapsulated with the cell. Following the 10x Genomics user manual's guidelines the droplets were directly subjected to reverse transcription the emulsion was broken and cDNA was purified using Silane beads. post the amplification of cDNA with 13 cycles purification and quantification were performed. The 10X Genomics single cell RNA sequencing library preparation – involving fragmentation dA …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP502616			RIS_F63_0007_P24_V14_S12_R1_001.fastq.gz RIS_F63_0007_P24_V14_S12_R2_001.fastq.gz	fastq fastq	16952946304.0	132444893.0	GSM8215879 r4	0:28 1:100	A:4861826090;C:3617895656;G:3887527721;T:4585054991;N:641846	28	100			4861826090	3617895656	3887527721	4585054991	641846	SRX24301539	SRS21065459	SRA1848620	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	Laboratory of Bioinformatics, Institute of Bioorganic Chemistry PAS	2	0.01258	0.89409	0.00497	0.2979	0.98888	0.77648	0.2572	0.55418	28	100	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Poland	2024-04-18	Larval	Larval	Head	Nervous System
31963	31963	SRR28832522	SRX24395271	SRS21150709	SRP504662	PRJNA1105232	Loss of alpha Ba crystallin but not alpha A crystallin increases age related cataract in the zebrafish lens	PRJNA1105232	Other	The vertebrate eye lens is an unusual organ in that most of its cells lack nuclei and the ability to replace aging protein. The small heat shock protein alpha crystallins evolved to become key components of this lens possibly because of their ability to prevent aggregation of aging protein that would otherwise lead to lens opacity. Most vertebrates express two alpha crystallins alpha A and alpha B crystallin and mutations in each are linked to human cataract. In a mouse knockout model only the loss of alpha A crystallin led to early stage lens cataract. We have used the zebrafish as a model system to investigate the role of alpha crystallins during lens development. Interestingly while zebrafish express one lens specific alpha A crystallin gene cryaa they express two alpha B crystallin genes with one evolving lens specificity cryaba and the other retaining the broad expression of its mammalian ortholog cryabb. In this study we used individual mutant zebrafish lines for all three alpha crystallin genes to determine the impact of their loss on age related cataract. Surprisingly unlike mouse knockout models we found that the loss of the alpha Ba crystallin gene cryaba led to an increase in lens opacity compared to cryaa null fish at 24 month of age. Loss of alpha A crystallin did not increase the prevalence of cataract. We also used single cell RNA Seq and RT qPCR data to show a shift in the lens expression of zebrafish alpha crystallins between 5 dpf and 10 dpf dpf with 5 dpf and 6 dpf lenses expressing cryaa almost exclusively and expression of cryaba and cryabb becoming more prominent post 10 dpf. These data show that cryaa is the primary alpha crystallin during early lens development while the protective role for cryaba becomes more important during lens aging. This study is the first to quantify cataract prevalence in wild type zebrafish showing that lens opacities develop in approximately 25% of fish by 18 month of age. None of the three alpha crystallin mutants showed a compensatory increase in t…					7b		strain:ABC\|dev stage:7 dpf\|collection date:2020 10\|geo loc name:USA: Oregon\|sex:N/A\|tissue:whole larvae\|treatment:replicate B\|BioSampleModel:Model organism or animal								scRNA seq of whole zebrafish larvae	7b	7b	10X Chromium			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP504662			7b_concatenated_R1.fastq.gz 7b_concatenated_R2.fastq.gz	fastq fastq	67688938179.0	524720451.0	7b concatenated R1.fastq.gz	0:28 1:101	A:18993507272;C:15386021146;G:15634918803;T:17652028346;N:22462612	28	101			18993507272	15386021146	15634918803	17652028346	22462612	SRX24395271	SRS21150709	SRA1854140	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	hiseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2024-04-29	Larval	Larval	Whole Organism	All anatomical structures

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