metadata: run_metadata: 178 rows where experiment.library_layout = "PAIRED", tissue_curation = "Spinal Cord" and tissue_curation

178 rows where experiment.library_layout = "PAIRED", tissue_curation = "Spinal Cord" and tissue_curation_coarse = "Nervous System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.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
44	44	DRR668250	DRX648352	DRS458865	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 3	Zebrafish 2wpi 3	SAMD00799623		sample name:Zebrafish 2wpi 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 25\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799623	DRX648352	RNA seq of spinal cord in zebrafish at 2wpi injured 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799623				14782516800.0	73912584.0	DRR668250	0:100 1:100	A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943	100	100		4058090278	3335994894	3323563782	4062467903	2399943	DRX648352	DRS458865	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
45	45	DRR668249	DRX648351	DRS458864	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 2	Zebrafish 2wpi 2	SAMD00799622		sample name:Zebrafish 2wpi 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799622	DRX648351	RNA seq of spinal cord in zebrafish at 2wpi injured 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799622				13687641800.0	68438209.0	DRR668249	0:100 1:100	A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902	100	100		3759784620	3087398782	3083881581	3754378915	2197902	DRX648351	DRS458864	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
46	46	DRR668248	DRX648350	DRS458863	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 1	Zebrafish 2wpi 1	SAMD00799621		sample name:Zebrafish 2wpi 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799621	DRX648350	RNA seq of spinal cord in zebrafish at 2wpi injured 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799621				16376197200.0	81880986.0	DRR668248	0:100 1:100	A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189	100	100		4485868844	3700974430	3710833937	4475827800	2692189	DRX648350	DRS458863	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
47	47	DRR668247	DRX648349	DRS458862	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish Intact biological replicate 3	Zebrafish Control 3	SAMD00799620		sample name:Zebrafish Control 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799620	DRX648349	RNA seq of spinal cord in zebrafish at 0wpi control 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799620				13377538600.0	66887693.0	DRR668247	0:100 1:100	A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800	100	100		3725064764	2973653932	2980883214	3695767890	2168800	DRX648349	DRS458862	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
48	48	DRR668246	DRX648348	DRS458861	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish Intact biological replicate 2	Zebrafish Control 2	SAMD00799619		sample name:Zebrafish Control 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799619	DRX648348	RNA seq of spinal cord in zebrafish at 0wpi control 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799619				14971411400.0	74857057.0	DRR668246	0:100 1:100	A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904	100	100		4160326445	3329083037	3329123314	4150453700	2424904	DRX648348	DRS458861	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
49	49	DRR668245	DRX648347	DRS458860	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.		pubmed:40278963	Zebrafish Intact biological replicate 1	Zebrafish Control 1	SAMD00799618		sample name:Zebrafish Control 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2024 05 04\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799618	DRX648347	RNA seq of spinal cord in zebrafish at 0wpi control 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799618				13912523800.0	69562619.0	DRR668245	0:100 1:100	A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776	100	100		3888902049	3079617959	3075111814	3866655202	2236776	DRX648347	DRS458860	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
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
24967	24967	SRR25557924	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5_S3_L001_I1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L001_R1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L001_R2_001.fastq.gz	fastq fastq fastq	783833459.0	6171917.0	GSM7688796 r1	0:8 1:28 2:91	A:165863131;C:117191802;G:128146802;T:150173329;N:269383	8	28	91	165863131	117191802	128146802	150173329	269383	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89127		0.221		0.78317		0.52195		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24968	24968	SRR25557925	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-3_S2_L002_I1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L002_R1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7208342327.0	56758601.0	GSM7688796 r10	0:8 1:28 2:91	A:1518008610;C:1083228714;G:1190089577;T:1369772782;N:3933008	8	28	91	1518008610	1083228714	1190089577	1369772782	3933008	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.88938		0.21991		0.79088		0.53044		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24969	24969	SRR25557926	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-3_S2_L003_I1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L003_R1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L003_R2_001.fastq.gz	fastq fastq fastq	7337435414.0	57775082.0	GSM7688796 r11	0:8 1:28 2:91	A:1545051667;C:1103394058;G:1211577972;T:1395133564;N:2375201	8	28	91	1545051667	1103394058	1211577972	1395133564	2375201	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.88966		0.2211		0.78961		0.53156		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24970	24970	SRR25557927	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-3_S2_L004_I1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L004_R1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L004_R2_001.fastq.gz	fastq fastq fastq	7218240453.0	56836539.0	GSM7688796 r12	0:8 1:28 2:91	A:1521442237;C:1084242714;G:1191469584;T:1372277539;N:2692975	8	28	91	1521442237	1084242714	1191469584	1372277539	2692975	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.8888		0.2174		0.79172		0.53311		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24971	24971	SRR25557928	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5_S3_L002_I1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L002_R1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L002_R2_001.fastq.gz	fastq fastq fastq	774302109.0	6096867.0	GSM7688796 r2	0:8 1:28 2:91	A:163989105;C:115793536;G:126358958;T:148430473;N:242825	8	28	91	163989105	115793536	126358958	148430473	242825	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89371		0.2215		0.78253		0.53282		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24972	24972	SRR25557929	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5_S3_L003_I1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L003_R1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L003_R2_001.fastq.gz	fastq fastq fastq	790430093.0	6223859.0	GSM7688796 r3	0:8 1:28 2:91	A:167465790;C:118269595;G:129024496;T:151447225;N:164063	8	28	91	167465790	118269595	129024496	151447225	164063	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89284		0.21955		0.78356		0.53369		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24973	24973	SRR25557930	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5_S3_L004_I1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L004_R1_001.fastq.gz MUTSU2_AllGFP-S5_S3_L004_R2_001.fastq.gz	fastq fastq fastq	778936974.0	6133362.0	GSM7688796 r4	0:8 1:28 2:91	A:165013558;C:116498474;G:127146290;T:149314806;N:162814	8	28	91	165013558	116498474	127146290	149314806	162814	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89195		0.2209		0.78196		0.53121		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24974	24974	SRR25557931	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-2_S2_L001_I1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L001_R1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L001_R2_001.fastq.gz	fastq fastq fastq	4174244890.0	32868070.0	GSM7688796 r5	0:8 1:28 2:91	A:882060228;C:627098568;G:684890393;T:795503862;N:1441319	8	28	91	882060228	627098568	684890393	795503862	1441319	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89137		0.22041		0.77926		0.52991		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24975	24975	SRR25557932	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-2_S2_L002_I1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L002_R1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L002_R2_001.fastq.gz	fastq fastq fastq	4150210902.0	32678826.0	GSM7688796 r6	0:8 1:28 2:91	A:878218072;C:623662333;G:679977758;T:790589138;N:1325865	8	28	91	878218072	623662333	679977758	790589138	1325865	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.89264		0.22159		0.78121		0.52989		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24976	24976	SRR25557933	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-2_S2_L003_I1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L003_R1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L003_R2_001.fastq.gz	fastq fastq fastq	4198043547.0	33055461.0	GSM7688796 r7	0:8 1:28 2:91	A:888287475;C:630914324;G:688006958;T:799794077;N:1044117	8	28	91	888287475	630914324	688006958	799794077	1044117	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.8912		0.21889		0.7822		0.52774		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24977	24977	SRR25557934	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-2_S2_L004_I1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L004_R1_001.fastq.gz MUTSU2_AllGFP-S5-2_S2_L004_R2_001.fastq.gz	fastq fastq fastq	4154784553.0	32714839.0	GSM7688796 r8	0:8 1:28 2:91	A:880520885;C:624179045;G:680076172;T:791297938;N:976309	8	28	91	880520885	624179045	680076172	791297938	976309	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.8927		0.22063		0.78216		0.5346		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24978	24978	SRR25557935	SRX21286763	SRS18536876	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 AllGFP S5	GSM7688796		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 AllGFP S5	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688796	GSM7688796: MUTSU2 AllGFP S5; Danio rerio; RNA Seq	GSM7688796 r1	GSM7688796	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_AllGFP-S5-3_S2_L001_I1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L001_R1_001.fastq.gz MUTSU2_AllGFP-S5-3_S2_L001_R2_001.fastq.gz	fastq fastq fastq	7231973725.0	56944675.0	GSM7688796 r9	0:8 1:28 2:91	A:1522035629;C:1085783001;G:1195535350;T:1374885853;N:3725592	8	28	91	1522035629	1085783001	1195535350	1374885853	3725592	SRX21286763	SRS18536876	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.88833		0.22076		0.79056		0.52744		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24979	24979	SRR25557936	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8_S2_L001_I1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L001_R1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L001_R2_001.fastq.gz	fastq fastq fastq	699161670.0	5505210.0	GSM7688795 r1	0:8 1:28 2:91	A:149927051;C:100829317;G:116075103;T:133908276;N:234363	8	28	91	149927051	100829317	116075103	133908276	234363	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85081		0.21257		0.80426		0.52779		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24980	24980	SRR25557937	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-3_S1_L002_I1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L002_R1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L002_R2_001.fastq.gz	fastq fastq fastq	8174836330.0	64368790.0	GSM7688795 r10	0:8 1:28 2:91	A:1748532358;C:1187854561;G:1356279755;T:1560491610;N:4401606	8	28	91	1748532358	1187854561	1356279755	1560491610	4401606	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85069		0.20989		0.81049		0.52069		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24981	24981	SRR25557938	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-3_S1_L003_I1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L003_R1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L003_R2_001.fastq.gz	fastq fastq fastq	8307872640.0	65416320.0	GSM7688795 r11	0:8 1:28 2:91	A:1778112295;C:1207569588;G:1377139686;T:1587359299;N:2704252	8	28	91	1778112295	1207569588	1377139686	1587359299	2704252	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85151		0.21054		0.80813		0.52675		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24982	24982	SRR25557939	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-3_S1_L004_R2_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L004_R1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L004_I1_001.fastq.gz	fastq fastq fastq	8197523483.0	64547429.0	GSM7688795 r12	0:8 1:28 2:91	A:1755321680;C:1190415496;G:1359502433;T:1565500310;N:3076120	8	28	91	1755321680	1190415496	1359502433	1565500310	3076120	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.84956		0.20968		0.81113		0.52382		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24983	24983	SRR25557940	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8_S2_L002_R2_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L002_R1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L002_I1_001.fastq.gz	fastq fastq fastq	690198899.0	5434637.0	GSM7688795 r2	0:8 1:28 2:91	A:147896108;C:99606794;G:114681063;T:132140792;N:227210	8	28	91	147896108	99606794	114681063	132140792	227210	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85228		0.21261		0.803		0.52382		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24984	24984	SRR25557941	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8_S2_L003_I1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L003_R1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L003_R2_001.fastq.gz	fastq fastq fastq	702239515.0	5529445.0	GSM7688795 r3	0:8 1:28 2:91	A:150477574;C:101266550;G:116878466;T:134415299;N:141606	8	28	91	150477574	101266550	116878466	134415299	141606	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85364		0.21344		0.80346		0.52158		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24985	24985	SRR25557942	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8_S2_L004_I1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L004_R1_001.fastq.gz MUTSU2_OtherGFP-G8_S2_L004_R2_001.fastq.gz	fastq fastq fastq	694537346.0	5468798.0	GSM7688795 r4	0:8 1:28 2:91	A:148876263;C:100202441;G:115455212;T:132982029;N:144673	8	28	91	148876263	100202441	115455212	132982029	144673	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85238		0.2138		0.80379		0.52691		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24986	24986	SRR25557943	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-2_S1_L001_R2_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L001_R1_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L001_I1_001.fastq.gz	fastq fastq fastq	4324997954.0	34055102.0	GSM7688795 r5	0:8 1:28 2:91	A:924471384;C:626141120;G:722856562;T:824050239;N:1494977	8	28	91	924471384	626141120	722856562	824050239	1494977	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85083		0.21122		0.80472		0.524		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24987	24987	SRR25557944	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-2_S1_L002_R2_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L002_R1_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L002_I1_001.fastq.gz	fastq fastq fastq	4306232942.0	33907346.0	GSM7688795 r6	0:8 1:28 2:91	A:920615353;C:623090513;G:721201055;T:819291149;N:1370416	8	28	91	920615353	623090513	721201055	819291149	1370416	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85335		0.21315		0.80206		0.51508		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24988	24988	SRR25557945	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-2_S1_L003_R2_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L003_R1_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L003_I1_001.fastq.gz	fastq fastq fastq	4348436312.0	34239656.0	GSM7688795 r7	0:8 1:28 2:91	A:930204208;C:629005094;G:727756813;T:827747478;N:1095103	8	28	91	930204208	629005094	727756813	827747478	1095103	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85369		0.21216		0.80503		0.52219		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24989	24989	SRR25557946	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-2_S1_L004_R2_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L004_R1_001.fastq.gz MUTSU2_OtherGFP-G8-2_S1_L004_I1_001.fastq.gz	fastq fastq fastq	4313915172.0	33967836.0	GSM7688795 r8	0:8 1:28 2:91	A:922742754;C:623127831;G:724345885;T:819819593;N:1037013	8	28	91	922742754	623127831	724345885	819819593	1037013	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.85456		0.21236		0.80223		0.5216		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
24990	24990	SRR25557947	SRX21286762	SRS18536875	SRP453891	PRJNA1003032	Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in These Cells. [scRNA Seq]	GSE240239	Transcriptome Analysis	Background: V0v spinal interneurons are highly conserved glutamatergic commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks we FAC sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression profiled them using microarrays and scRNA seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild type siblings. Results: Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that by this stage of development evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly we show that Hmx2/3a repress dI2 interneuronal expression of skor1a and nefma two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly distinct subsets of V0v spinal interneurons as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2 V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then later start to express markers of distinct types of inhibitory s…	parent bioproject:PRJNA1003022	pubmed:38017520		MUTSU2 OtherGFP G8	GSM7688795		source name:Spinal Cord\|tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1\|geo loc name:missing\|collection date:missing	MUTSU2 OtherGFP G8	We performed demultiplexing and counts analysis as per the manufacturer’s instructions using Cell Ranger v4.0.0 software https://www.10xgenomics.com We analyzed the data using Partek Flow Genomic Analysis Software https://www.partek.com/partek flow/. Multiplets were removed by filtering out cells with >12 000 counts and >2 500 detected genes. Sick and/or “leaky” cells were removed by filtering out cells with <500 detected genes and >6% mitochondrial transcripts. We normalized the data using a counts per million CPM algorithm and applied a logarithmic transformation to improve data visualization. The outcome of normalisation was assessed by principal components analysis PCA graph based clustering and Uniform Manifold Approximation and Projection UMAP plotting using the NN Descent method of nearest neighbour type calculation and Euclidean distance metrics. We manually inspected UMAP plots to assess clustering quality based on expression of known V0v spinal interneuron markers. We then fine tuned the clustering by manually deducing and extrapolating cell fate assignments by comparing expression profiles of 48 hpf single cell clusters with the molecular phenotypes of V0v spinal interneurons in 24 hpf and 30 hpf wild type evx1i232 and evx2sa140 single mutant and evx1i232;evx2sa140 double mutant embryos. To perform differential expression analysis in Partek Flow we used the statistically robust Hurdle Model two part model with default parameters. We initially analyzed the two libraries separately. We then combined the data from these two libraries using the Counts Aggregation pipeline in Cell Ranger v4.0.0 and reanalyzed the data as described above. Assembly: Lawson Lab zebrafish transcriptome V4.3.2 https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ Supplementary files format and content: Tab separated and matrix files.	Spinal Cord		Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz’s L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…	Embryos obtained from crossing heterozygous evx1i232/+;evx2sa140/+;Tgevx1:EGFPSU2 parents were raised at 28.5oC until they reached the desired developmental stage of 48 hpf as confirmed by analysis of morphological criteria including head trunk angle head and eye size.	tissue:Spinal Cord\|cell line:Tgevx1:EGFPSU2\|cell type:V0v spinal interneurons\|genotype:evx1i232/+;evx2sa140/+ incross\|treatment:N1	GSM7688795	GSM7688795: MUTSU2 OtherGFP G8; Danio rerio; RNA Seq	GSM7688795 r1	GSM7688795	1	Embryos were screened for fluorescence from 30 hpf onwards using a fluorescent dissecting microscope. Only EGFP positive embryos were used for dissections and FACS at 48 hpf. Embryos were deyolked dissected and dissociated as described in GSE145916 with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord and posteriorly immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System Worthington Biochemical Corporation LK003150 trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 40 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately post homogenising the digested tissue mixture with a sterile p200 tip we passed each sample through a 40 µm Flowmi cell strainer Merck BAH136800040 into a sterile microcentrifuge tube. post Papain inactivation samples were resuspended in 1 ml Leibovitz's L 15 medium ThermoFisher Scientific 21083027 + 0.5% FBS and stored on ice. Immediately before FACS DAPI Merck D9542 and Draq5 BioLegend 424101 were added at a final concentration of 5 µg/ml and 5 µM respectively. FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al. 2008 with the following modifications. Ice cold samples were filtered through 35 µm mesh strainers in to 5 ml round bottomed polystyrene tubes Corning Falcon 352235. All FAC sorting and collection steps were performed at +4oC using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates forward scatter height x forward scatter width followed by side scatter height x side scatter width were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI negative sick cells are DAPI permeant…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP453891		loader:fastq load.py	MUTSU2_OtherGFP-G8-3_S1_L001_R2_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L001_R1_001.fastq.gz MUTSU2_OtherGFP-G8-3_S1_L001_I1_001.fastq.gz	fastq fastq fastq	8184961024.0	64448512.0	GSM7688795 r9	0:8 1:28 2:91	A:1748819280;C:1187802244;G:1360994184;T:1562975470;N:4223414	8	28	91	1748819280	1187802244	1360994184	1562975470	4223414	SRX21286762	SRS18536875	SRA1688438	Lewis Lab, Biology, Syracuse University	Lewis Lab, Biology, Syracuse University	1	0.8493		0.21072		0.80967		0.52593		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-08-07	Multi-stage	Embryo	Spinal Cord	Nervous System
55972	55972	SRR10895875	SRX7564604	SRS6001805	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.		pubmed:33545088;pubmed:12470943			Zebrafish 009		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Spinal cord\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : adult	CL100103178 L01 9	CL100103178 L01 9				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982			CL100103178_L01_567_1.fq.gz CL100103178_L01_567_2.fq.gz	fastq fastq	7926659000.0	79266590.0	CL100103178 L01 567 1.fq.gz	0:100 1:100	A:2177233520;C:1750763335;G:1793690428;T:2195598681;N:9373036	100	100		2177233520	1750763335	1793690428	2195598681	9373036	SRX7564604	SRS6001805	SRA1026516	BGI\|BGI-Research	BGI	1	0.90731		0.11069		0.70548		0.53521		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Spinal Cord	Nervous System
55973	55973	SRR10895876	SRX7564603	SRS6001805	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.		pubmed:33545088;pubmed:12470943			Zebrafish 009		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Spinal cord\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : adult	CL100103178 L01 8	CL100103178 L01 8				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982			CL100103178_L01_563_1.fq.gz CL100103178_L01_563_2.fq.gz	fastq fastq	9981278800.0	99812788.0	CL100103178 L01 563 1.fq.gz	0:100 1:100	A:2753622693;C:2192952746;G:2243702494;T:2779006876;N:11993991	100	100		2753622693	2192952746	2243702494	2779006876	11993991	SRX7564603	SRS6001805	SRA1026516	BGI\|BGI-Research	BGI	1	0.90715		0.11372		0.71467		0.5089		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Spinal Cord	Nervous System
55974	55974	SRR10895877	SRX7564602	SRS6001805	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.		pubmed:33545088;pubmed:12470943			Zebrafish 009		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Spinal cord\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : adult	CL100103178 L01 7	CL100103178 L01 7				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982			CL100103178_L01_562_1.fq.gz CL100103178_L01_562_2.fq.gz	fastq fastq	8857552800.0	88575528.0	CL100103178 L01 562 1.fq.gz	0:100 1:100	A:2418167382;C:1969456035;G:2015821568;T:2442764114;N:11343701	100	100		2418167382	1969456035	2015821568	2442764114	11343701	SRX7564602	SRS6001805	SRA1026516	BGI\|BGI-Research	BGI	1	0.90895		0.10978		0.71336		0.50272		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Spinal Cord	Nervous System
55975	55975	SRR10895878	SRX7564601	SRS6001805	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.		pubmed:33545088;pubmed:12470943			Zebrafish 009		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Spinal cord\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : adult	CL100103178 L01 6	CL100103178 L01 6				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982			CL100103178_L01_564_1.fq.gz CL100103178_L01_564_2.fq.gz	fastq fastq	7468499200.0	74684992.0	CL100103178 L01 564 1.fq.gz	0:100 1:100	A:2052720985;C:1649448011;G:1690698471;T:2068073830;N:7557903	100	100		2052720985	1649448011	1690698471	2068073830	7557903	SRX7564601	SRS6001805	SRA1026516	BGI\|BGI-Research	BGI	1	0.90905		0.10883		0.69578		0.54193		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Spinal Cord	Nervous System
55976	55976	SRR10895881	SRX7564598	SRS6001805	SRP241982	PRJNA599026	Project of basal ray finned fishes	PRJNA599026	Other	The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.		pubmed:33545088;pubmed:12470943			Zebrafish 009		strain:not collected\|isolate:not collected\|breed:not collected\|cultivar:not collected\|ecotype:not collected\|age:not collected\|dev stage:Adult\|sex:not determined\|tissue:Spinal cord\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : adult	CL100103178 L01 5	CL100103178 L01 5				RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP241982			CL100103178_L01_561_1.fq.gz CL100103178_L01_561_2.fq.gz	fastq fastq	9173572800.0	91735728.0	CL100103178 L01 561 1.fq.gz	0:100 1:100	A:2527132650;C:2020739240;G:2066720461;T:2548747865;N:10232584	100	100		2527132650	2020739240	2066720461	2548747865	10232584	SRX7564598	SRS6001805	SRA1026516	BGI\|BGI-Research	BGI	1	0.91539		0.11063		0.71427		0.48162		100		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-01-15	Adult	Adult	Spinal Cord	Nervous System
60587	60587	SRR12424278	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_1_S41_L001_R1_001.fastq.gz olig2_egfp_48hpf_1_S41_L001_R2_001.fastq.gz	fastq fastq	18778651430.0	62180965.0	GSM4718658 r1	0:151 1:151	A:6542554044;C:3515052559;G:3489753648;T:5231107020;N:184159	151	151		6542554044	3515052559	3489753648	5231107020	184159	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90055	0.0	0.21162	1.0	0.77776		0.53718	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60588	60588	SRR12424279	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_2_S42_L001_R1_001.fastq.gz olig2_egfp_48hpf_2_S42_L001_R2_001.fastq.gz	fastq fastq	22242782898.0	73651599.0	GSM4718658 r2	0:151 1:151	A:7753674261;C:4160150132;G:4127581173;T:6201157562;N:219770	151	151		7753674261	4160150132	4127581173	6201157562	219770	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90097	0.0	0.2127	1.0	0.77966		0.54192	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60589	60589	SRR12424280	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_3_S43_L001_R2_001.fastq.gz olig2_egfp_48hpf_3_S43_L001_R1_001.fastq.gz	fastq fastq	25591190986.0	84739043.0	GSM4718658 r3	0:151 1:151	A:8917343424;C:4797392797;G:4757647263;T:7118554564;N:252938	151	151		8917343424	4797392797	4757647263	7118554564	252938	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90089	0.0	0.2095	1.0	0.78078		0.53755	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60590	60590	SRR12424281	SRX8920145	SRS7176693	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 48hpf	GSM4718658		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718658	GSM4718658: scRNAseq olig2 eGFP 48hpf; Danio rerio; RNA Seq	GSM4718658		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			olig2_egfp_48hpf_4_S44_L001_R1_001.fastq.gz olig2_egfp_48hpf_4_S44_L001_R2_001.fastq.gz	fastq fastq	25546281170.0	84590335.0	GSM4718658 r4	0:151 1:151	A:8905009196;C:4774524700;G:4734395060;T:7132103501;N:248713	151	151		8905009196	4774524700	4734395060	7132103501	248713	SRX8920145	SRS7176693	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.90169	0.0	0.21158	1.0	0.77697		0.54006	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Hatching	Embryo	Spinal Cord	Nervous System
60591	60591	SRR12424274	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_1_S69_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_1_S69_L001_R2_001.fastq.gz	fastq fastq	13366864582.0	44261141.0	GSM4718657 r1	0:151 1:151	A:3721647646;C:2385939960;G:3494552257;T:3764514262;N:210457	151	151		3721647646	2385939960	3494552257	3764514262	210457	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.85449	0.0	0.08264	1.0	0.84086		0.50156	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60592	60592	SRR12424275	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_2_S70_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_2_S70_L001_R2_001.fastq.gz	fastq fastq	10606211914.0	35119907.0	GSM4718657 r2	0:151 1:151	A:2974656607;C:1869869441;G:2750621038;T:3010898673;N:166155	151	151		2974656607	1869869441	2750621038	3010898673	166155	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.84822	0.0	0.08456	1.0	0.83719		0.51503	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60593	60593	SRR12424276	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_3_S71_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_3_S71_L001_R2_001.fastq.gz	fastq fastq	15614508642.0	51703671.0	GSM4718657 r3	0:151 1:151	A:4330312984;C:2826855730;G:4093245712;T:4363847925;N:246291	151	151		4330312984	2826855730	4093245712	4363847925	246291	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.8543	0.0	0.08219	1.0	0.83727		0.51892	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60594	60594	SRR12424277	SRX8920144	SRS7176692	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 36hpf	GSM4718657		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718657	GSM4718657: scRNAseq olig2 eGFP 36hpf; Danio rerio; RNA Seq	GSM4718657		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_36hfp_4_S72_L001_R1_001.fastq.gz Olig2_eGFP_36hfp_4_S72_L001_R2_001.fastq.gz	fastq fastq	10707787198.0	35456249.0	GSM4718657 r4	0:151 1:151	A:2981466900;C:1909696186;G:2797297473;T:3019156550;N:170089	151	151		2981466900	1909696186	2797297473	3019156550	170089	SRX8920144	SRS7176692	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.85466	0.0	0.08381	1.0	0.83562		0.51035	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60595	60595	SRR12424270	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_1_S10_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_1_S10_L001_R2_001.fastq.gz	fastq fastq	21279021170.0	70460335.0	GSM4718656 r1	0:151 1:151	A:5842145219;C:3712477572;G:5933108587;T:5790922441;N:367351	151	151		5842145219	3712477572	5933108587	5790922441	367351	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83071	0.0	0.06828	1.0	0.8406		0.5078	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60596	60596	SRR12424271	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_2_S20_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_2_S20_L001_R2_001.fastq.gz	fastq fastq	22414094210.0	74218855.0	GSM4718656 r2	0:151 1:151	A:6145677154;C:3904876630;G:6254105391;T:6109049174;N:385861	151	151		6145677154	3904876630	6254105391	6109049174	385861	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83148	0.0	0.06914	1.0	0.84033		0.49666	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60597	60597	SRR12424272	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_3_S30_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_3_S30_L001_R2_001.fastq.gz	fastq fastq	16406166006.0	54325053.0	GSM4718656 r3	0:151 1:151	A:4513103872;C:2865727260;G:4569430659;T:4457621166;N:283049	151	151		4513103872	2865727260	4569430659	4457621166	283049	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.82928	0.0	0.06878	1.0	0.83989		0.4916	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
60598	60598	SRR12424273	SRX8920143	SRS7176691	SRP276929	PRJNA656271	Single cell RNA seq analysis of pMN neural progenitors from zebrafish	GSE155988	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:32680935		scRNAseq olig2 eGFP 24hpf	GSM4718656		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf	Raw sequencing reads were demultiplexed mapped to the zebrafish reference genome and summarized into gene expression matrices using CellRanger version 3.0.1 Count matrices were further filtered in Seurat 3.1.0 https://satijalab.org/seurat/ to remove cell barcodes with fewer than 250 detectable genes more than 5% of UMIs derived from mitochondrial genes or more than 50 000 UMIs to exclude putative doublets Standard Seurat normalization and PCA was run using the 1 291 most variable genes Applied Harmony https://doi.org/10.1038/s41592 019 0619 0 alignment theta = 2 to correct for inter sample variation chose 20 Harmony dimensions and applied Seurat UMAP reduction Genome build: GRCz11 Supplementary files format and content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM4718656	GSM4718656: scRNAseq olig2 eGFP 24hpf; Danio rerio; RNA Seq	GSM4718656		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM4718656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP276929			Olig2_eGFP_24hfp_4_S40_L001_R1_001.fastq.gz Olig2_eGFP_24hfp_4_S40_L001_R2_001.fastq.gz	fastq fastq	17382967792.0	57559496.0	GSM4718656 r4	0:151 1:151	A:4767137063;C:3044788720;G:4846983492;T:4723757048;N:301469	151	151		4767137063	3044788720	4846983492	4723757048	301469	SRX8920143	SRS7176691	SRA1111061	GEO	University of Colorado School of Medicine	2	0.0	0.83084	0.0	0.06779	1.0	0.83948		0.49689	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-08-10	Pharyngula	Embryo	Spinal Cord	Nervous System
62942	62942	SRR13447021	SRX9860257	SRS8040688	SRP301983	PRJNA692494	Localized EMT reprograms glial progenitors to promote spinal cord repair [single cell RNA seq]	GSE164944	Other	Single nuclear RNA sequencing was performed on spinal cord tissues from Tggfap:EGFP zebrafish at 1 xxx post injury using the 10x Genomics platform. Overall design: Single nuclear RNA sequencing of spinal cord tissue.	parent bioproject:PRJNA692492	pubmed:33609461		single cell injured spinal cord	GSM5023610		tissue:5 xxx post injury spinal cord nuclear\|tissues:spinal cord\|rna population:nuclear\|time point:5 xxx post injury	single cell injured spinal cord	Aligned reads were analyzed using the Seurat package v3.1.4 within R v3.6.3. Cells that have unique number of genes between 200 to 4000 and a mitochondrial gene percentage less than five were filtered. The “SCTransform” function was used for normalization scaling and finding variable features. SCTransform returned 3000 highly variable features for downstream analysis. Significant principal components were determined using “ElbowPlot” function. Forty principal components were selected to create a Shared Nearest Neighbour SNN graph using the “FindNeighbours” function. Clustering was performed by the Louvain algorithm using the function “FindClusters” and the resolution parameter was set to one. Uniform Manifold Approximation and Reduction UMAP was used for non linear dimensional reduction of the first 40 principle components and to visualize the data in two dimensional space “RunUMAP” function Differential gene expression for individual cluster was identified using Wilcoxon rank sum tests in the “FindAllMarkers” function. Supplementary files format and content: RDS file	5 xxx post injury spinal cord nuclear	Adult zebrafish were subjected to complete spinal cord transection.	gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.		tissues:spinal cord\|rna population:nuclear\|time point:5 xxx post injury	GSM5023610	GSM5023610: single cell injured spinal cord; Danio rerio; RNA Seq	GSM5023610		1	gfap:EGFP transgenic animals were subjected to SCI and 2 mm SC tissue sections spanning the lesion site were collected at 1 wpi. Nuclei were isolated from 45 pooled SC tissues. For single nuclear library preparation on the 10x Genomics platform the Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 cat# 1000092 and the Chromium Chip B Single Cell Kit cat# 1000074 were used according to the manufacturer's instructions in the Chromium Single Cell 3′ Reagents Kits V3 User Guide. The resulting cDNA libraries were quantified on an Agilent Tapestation and sequenced on Illumina HiSeq 3000.	GEO Accession:GSM5023610	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP301983		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=ZB nuc S1 L007 I1 001.fastq.gz read2PairFiles=ZB nuc S1 L007 R1 001.fastq.gz read3PairFiles=ZB nuc S1 L007 R2 001.fastq.gz	ZB_nuc_S1_L007_R2_001.fastq.gz ZB_nuc_S1_L007_R1_001.fastq.gz ZB_nuc_S1_L007_I1_001.fastq.gz	fastq fastq fastq	134333186988.0	436146711.0	GSM5023610 r1	0:8 1:150 2:150	A:34573306207;C:23174725516;G:24790836286;T:51771968988;N:22349991	8	150	150	34573306207	23174725516	24790836286	51771968988	22349991	SRX9860257	SRS8040688	SRA1184553	GEO	Developmental Biology, Washington University	1	0.72186		0.41754		0.80551		0.54979		150		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-01-15	Adult	Adult	Spinal Cord	Nervous System
64205	64205	SRR14326888	SRX10681834	SRS8775213	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 48hpf [reanalysis]	GSM5266260		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266260	GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266260		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			olig2_egfp_48hpf_1_S41_L001_R1_001.fastq olig2_egfp_48hpf_1_S41_L001_R2_001.fastq	fastq fastq	18778651430.0	62180965.0	GSM5266260 r1	0:151 1:151	A:6542554044;C:3515052559;G:3489753648;T:5231107020;N:184159	151	151		6542554044	3515052559	3489753648	5231107020	184159	SRX10681834	SRS8775213	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.90056	0.0	0.21167	1.0	0.7781		0.53738	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Hatching	Embryo	Spinal Cord	Nervous System
64206	64206	SRR14326889	SRX10681834	SRS8775213	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 48hpf [reanalysis]	GSM5266260		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266260	GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266260		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			olig2_egfp_48hpf_2_S42_L001_R1_001.fastq olig2_egfp_48hpf_2_S42_L001_R2_001.fastq	fastq fastq	22242782898.0	73651599.0	GSM5266260 r2	0:151 1:151	A:7753674261;C:4160150132;G:4127581173;T:6201157562;N:219770	151	151		7753674261	4160150132	4127581173	6201157562	219770	SRX10681834	SRS8775213	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.90096	0.0	0.21256	1.0	0.77928		0.54059	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Hatching	Embryo	Spinal Cord	Nervous System
64207	64207	SRR14326890	SRX10681834	SRS8775213	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 48hpf [reanalysis]	GSM5266260		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266260	GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266260		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			olig2_egfp_48hpf_3_S43_L001_R2_001.fastq olig2_egfp_48hpf_3_S43_L001_R1_001.fastq	fastq fastq	25591190986.0	84739043.0	GSM5266260 r3	0:151 1:151	A:8917343424;C:4797392797;G:4757647263;T:7118554564;N:252938	151	151		8917343424	4797392797	4757647263	7118554564	252938	SRX10681834	SRS8775213	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.90089	0.0	0.20934	1.0	0.78086		0.53725	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Hatching	Embryo	Spinal Cord	Nervous System
64208	64208	SRR14326891	SRX10681834	SRS8775213	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 48hpf [reanalysis]	GSM5266260		tissue:spinal cord cells\|developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 48hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:48 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266260	GSM5266260: scRNAseq olig2 eGFP 48hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266260		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266260	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			olig2_egfp_48hpf_4_S44_L001_R1_001.fastq olig2_egfp_48hpf_4_S44_L001_R2_001.fastq	fastq fastq	25546281170.0	84590335.0	GSM5266260 r4	0:151 1:151	A:8905009196;C:4774524700;G:4734395060;T:7132103501;N:248713	151	151		8905009196	4774524700	4734395060	7132103501	248713	SRX10681834	SRS8775213	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.90171	0.0	0.21154	1.0	0.77674		0.53902	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Hatching	Embryo	Spinal Cord	Nervous System
64209	64209	SRR14326884	SRX10681833	SRS8775212	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 36hpf [reanalysis]	GSM5266259		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266259	GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266259		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_36hfp_1_S69_L001_R1_001.fastq Olig2_eGFP_36hfp_1_S69_L001_R2_001.fastq	fastq fastq	13366864582.0	44261141.0	GSM5266259 r1	0:151 1:151	A:3721647646;C:2385939960;G:3494552257;T:3764514262;N:210457	151	151		3721647646	2385939960	3494552257	3764514262	210457	SRX10681833	SRS8775212	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.85451	0.0	0.08269	1.0	0.84094		0.5016	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64210	64210	SRR14326885	SRX10681833	SRS8775212	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 36hpf [reanalysis]	GSM5266259		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266259	GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266259		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_36hfp_2_S70_L001_R1_001.fastq Olig2_eGFP_36hfp_2_S70_L001_R2_001.fastq	fastq fastq	10606211914.0	35119907.0	GSM5266259 r2	0:151 1:151	A:2974656607;C:1869869441;G:2750621038;T:3010898673;N:166155	151	151		2974656607	1869869441	2750621038	3010898673	166155	SRX10681833	SRS8775212	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.84821	0.0	0.08459	1.0	0.83731		0.51513	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64211	64211	SRR14326886	SRX10681833	SRS8775212	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 36hpf [reanalysis]	GSM5266259		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266259	GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266259		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_36hfp_3_S71_L001_R1_001.fastq Olig2_eGFP_36hfp_3_S71_L001_R2_001.fastq	fastq fastq	15614508642.0	51703671.0	GSM5266259 r3	0:151 1:151	A:4330312984;C:2826855730;G:4093245712;T:4363847925;N:246291	151	151		4330312984	2826855730	4093245712	4363847925	246291	SRX10681833	SRS8775212	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.85427	0.0	0.08218	1.0	0.83713		0.51889	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64212	64212	SRR14326887	SRX10681833	SRS8775212	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 36hpf [reanalysis]	GSM5266259		tissue:spinal cord cells\|developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 36hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:36 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266259	GSM5266259: scRNAseq olig2 eGFP 36hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266259		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266259	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_36hfp_4_S72_L001_R1_001.fastq Olig2_eGFP_36hfp_4_S72_L001_R2_001.fastq	fastq fastq	10707787198.0	35456249.0	GSM5266259 r4	0:151 1:151	A:2981466900;C:1909696186;G:2797297473;T:3019156550;N:170089	151	151		2981466900	1909696186	2797297473	3019156550	170089	SRX10681833	SRS8775212	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.85465	0.0	0.08381	1.0	0.8355		0.51049	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64213	64213	SRR14326880	SRX10681832	SRS8775211	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 24hpf [reanalysis]	GSM5266258		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266258	GSM5266258: scRNAseq olig2 eGFP 24hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266258		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_24hfp_1_S10_L001_R1_001.fastq Olig2_eGFP_24hfp_1_S10_L001_R2_001.fastq	fastq fastq	21279021170.0	70460335.0	GSM5266258 r1	0:151 1:151	A:5842145219;C:3712477572;G:5933108587;T:5790922441;N:367351	151	151		5842145219	3712477572	5933108587	5790922441	367351	SRX10681832	SRS8775211	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.83071	0.0	0.06834	1.0	0.8407		0.50743	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64214	64214	SRR14326881	SRX10681832	SRS8775211	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 24hpf [reanalysis]	GSM5266258		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266258	GSM5266258: scRNAseq olig2 eGFP 24hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266258		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_24hfp_2_S20_L001_R1_001.fastq Olig2_eGFP_24hfp_2_S20_L001_R2_001.fastq	fastq fastq	22414094210.0	74218855.0	GSM5266258 r2	0:151 1:151	A:6145677154;C:3904876630;G:6254105391;T:6109049174;N:385861	151	151		6145677154	3904876630	6254105391	6109049174	385861	SRX10681832	SRS8775211	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.83142	0.0	0.06899	1.0	0.84029		0.49666	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64215	64215	SRR14326882	SRX10681832	SRS8775211	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 24hpf [reanalysis]	GSM5266258		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266258	GSM5266258: scRNAseq olig2 eGFP 24hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266258		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_24hfp_3_S30_L001_R1_001.fastq Olig2_eGFP_24hfp_3_S30_L001_R2_001.fastq	fastq fastq	16406166006.0	54325053.0	GSM5266258 r3	0:151 1:151	A:4513103872;C:2865727260;G:4569430659;T:4457621166;N:283049	151	151		4513103872	2865727260	4569430659	4457621166	283049	SRX10681832	SRS8775211	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.8293	0.0	0.06878	1.0	0.84017		0.49152	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
64216	64216	SRR14326883	SRX10681832	SRS8775211	SRP316409	PRJNA725224	Single cell RNA seq analysis of pMN neural progenitors from zebrafish [Reanalysis of GSE155988 data set]	GSE173350	Transcriptome Analysis	The goal of this study was to identify distinct cell populations that arise from ventral spinal cord pMN progenitors. To do so we sorted fluorescently marked pMN cells obtained from Tgolig2:EGFP zebrafish embryos at 24 36 hpf and 48 hpf and performed 10X Chromium single cell RNA seq. Overall design: Three samples obtained from wild type zebrafish embryos at three developmental timepoints were analyzed.		pubmed:34303700		scRNAseq olig2 eGFP 24hpf [reanalysis]	GSM5266258		tissue:spinal cord cells\|developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	scRNAseq olig2 eGFP 24hpf [reanalysis]	Generated cell feature counts for each single cell RNAseq library using cellranger count transcriptome=GRCz11 Each single cell RNAseq sample was converted to a Seurat object using the Seurat Read 10X CreateSeuratObject functions 3 separate Seurat objects filtered individual Seurat objects to select cells with nGene >250 and percent.mitochondrial <5% and nFeature RNA <50000 hpf 24 hpf and 48 hpf samples or <30000 hpf 36 hpf Processed and filtered Seurat objects using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction 'pca' dims = 1:40 FindClustersresolution= 0.9 hpf 48 hpf; 1 hpf 36 hpf; 1.2 hpf 24 hpf dims = 1:40 and RunUMAPdims=1:40 Clusters with low nFeatures and high percent.mitochondrial reads were removed as dying cells in 24 hpf and 36 hpf datasets Individual processed Seurat objects from each sample were intergrated using the FindIntergrationAnchorsdims 1:40 and IntergrateDatadims = 1:40 Seurat functions Processed and filtered intergrated Seurat object using Seurat NormalizeData FindVariableFeaturesselection.method = 'vst' nfeatures = 2000 ScaleData vars.to.regress=c'nCount RNA' 'percent.mito' 'CC.difference' RunPCAnpcs=100 RunUMAPdims = 1:40 FindNeighborsreduction = 'pca' dims = 1:40 FindClustersresolution= 1.2 dims = 1:40 and RunUMAPdims=1:40 Genome build: GRCz11 Supplementary files format and content: gzipped rds file of intergrated Seurat object Supplementary files format and content: gzipped csv file of metadata for cells	spinal cord cells	No treatment was applied to the samples.	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	Embryos were raised at 28.5°C in E3 media 5 mM NaCl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 at pH 7.4 with sodium bicarbonate sorted for good health and staged accordingly to developmental morphological features and hpf	developmental stage:24 hpf ZFIN ID: ZDB ALT 041129 8	GSM5266258	GSM5266258: scRNAseq olig2 eGFP 24hpf [reanalysis]; Danio rerio; RNA Seq	GSM5266258		1	24 36 and 48 hpf Tgolig2:EGFP euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre chilled Ca free Ringers solution 116 mM NaCl 2.6 mM KCl 5 mM HEPES pH 7.0 on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution 10 mg/ml BI protease 125 U/ml DNase 2.5 mM EDTA 1X PBS was added to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution 30% FBS 0.8 mM CaCl2 1X PBS was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice 1 ml of chilled suspension media 1% FBS 0.8 mM CaCl2 50 U/ml Penicillin 0.05 mg/ml Streptomycin was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS. The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell three prime Reagent Kit part no. PN 1000075. Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.	GEO Accession:GSM5266258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP316409			Olig2_eGFP_24hfp_4_S40_L001_R1_001.fastq Olig2_eGFP_24hfp_4_S40_L001_R2_001.fastq	fastq fastq	17382967792.0	57559496.0	GSM5266258 r4	0:151 1:151	A:4767137063;C:3044788720;G:4846983492;T:4723757048;N:301469	151	151		4767137063	3044788720	4846983492	4723757048	301469	SRX10681832	SRS8775211	SRA1223938	GEO	Bruce Appel, Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus	2	0.0	0.83086	0.0	0.0679	1.0	0.83944		0.4968	151	151	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-26	Pharyngula	Embryo	Spinal Cord	Nervous System
65782	65782	SRR15626598	SRX11923661	SRS9937171	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP SC 5	GSM5538915		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP SC 5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538915	GSM5538915: SP SC 5; Danio rerio; RNA Seq	GSM5538915		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538915	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_SC_5_1.fq.gz SP_SC_5_2.fq.gz	fastq fastq	15123413700.0	50411379.0	GSM5538915 r1	0:150 1:150	A:4455675867;C:2762093028;G:3064816838;T:4839518034;N:1309933	150	150		4455675867	2762093028	3064816838	4839518034	1309933	SRX11923661	SRS9937171	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.87431	0.86943	0.22595	0.2251	0.80282	0.80663	0.54345	0.53283	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65783	65783	SRR15626597	SRX11923660	SRS9937170	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP SC 4	GSM5538914		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP SC 4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538914	GSM5538914: SP SC 4; Danio rerio; RNA Seq	GSM5538914		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538914	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_SC_4_1.fq.gz SP_SC_4_2.fq.gz	fastq fastq	16743046500.0	55810155.0	GSM5538914 r1	0:150 1:150	A:4990111476;C:2997789090;G:3379928547;T:5374081112;N:1136275	150	150		4990111476	2997789090	3379928547	5374081112	1136275	SRX11923660	SRS9937170	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.78972	0.78594	0.27052	0.26874	0.85013	0.85342	0.57347	0.57843	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65784	65784	SRR15626596	SRX11923659	SRS9937169	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP SC 3	GSM5538913		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP SC 3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538913	GSM5538913: SP SC 3; Danio rerio; RNA Seq	GSM5538913		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538913	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_SC_3_1.fq.gz SP_SC_3_2.fq.gz	fastq fastq	18816263700.0	62720879.0	GSM5538913 r1	0:150 1:150	A:5718449534;C:3326587767;G:3765533138;T:6005600414;N:92847	150	150		5718449534	3326587767	3765533138	6005600414	92847	SRX11923659	SRS9937169	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.85756	0.85572	0.21036	0.20882	0.85222	0.85441	0.42132	0.6499	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65785	65785	SRR15626595	SRX11923658	SRS9937168	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP SC 2	GSM5538912		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP SC 2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538912	GSM5538912: SP SC 2; Danio rerio; RNA Seq	GSM5538912		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538912	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_SC_2_1.fq.gz SP_SC_2_2.fq.gz	fastq fastq	17380791000.0	57935970.0	GSM5538912 r1	0:150 1:150	A:5260639203;C:3099491904;G:3440470486;T:5579887776;N:301631	150	150		5260639203	3099491904	3440470486	5579887776	301631	SRX11923658	SRS9937168	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.75526	0.75779	0.22658	0.22782	0.86111	0.86237	0.59826	0.60551	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65786	65786	SRR15626594	SRX11923657	SRS9937166	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP SC 1	GSM5538911		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP SC 1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segments distal to the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538911	GSM5538911: SP SC 1; Danio rerio; RNA Seq	GSM5538911		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538911	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_SC_1_1.fq.gz SP_SC_1_2.fq.gz	fastq fastq	20361678900.0	67872263.0	GSM5538911 r1	0:150 1:150	A:6177247371;C:3549700804;G:3997102203;T:6637296058;N:332464	150	150		6177247371	3549700804	3997102203	6637296058	332464	SRX11923657	SRS9937166	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.80835	0.80708	0.24946	0.25241	0.84037	0.84303	0.5988	0.59871	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65787	65787	SRR15626593	SRX11923656	SRS9937165	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 6	GSM5538910		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 6	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538910	GSM5538910: SP 6W 6; Danio rerio; RNA Seq	GSM5538910		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538910	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_6_1.fq.gz SP_6W_6_2.fq.gz	fastq fastq	22472709600.0	74909032.0	GSM5538910 r1	0:150 1:150	A:6919488736;C:3623491665;G:4350778578;T:7578832909;N:117712	150	150		6919488736	3623491665	4350778578	7578832909	117712	SRX11923656	SRS9937165	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.81992	0.81637	0.29919	0.29843	0.83309	0.83707	0.62577	0.60938	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65788	65788	SRR15626592	SRX11923655	SRS9937167	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 5	GSM5538909		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538909	GSM5538909: SP 6W 5; Danio rerio; RNA Seq	GSM5538909		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538909	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_5_1.fq.gz SP_6W_5_2.fq.gz	fastq fastq	20583610500.0	68612035.0	GSM5538909 r1	0:150 1:150	A:6360709506;C:3307195715;G:4004718826;T:6910881382;N:105071	150	150		6360709506	3307195715	4004718826	6910881382	105071	SRX11923655	SRS9937167	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.80493	0.80492	0.3258	0.3244	0.82682	0.83002	0.58555	0.58892	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65789	65789	SRR15626591	SRX11923654	SRS9937164	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 4	GSM5538908		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538908	GSM5538908: SP 6W 4; Danio rerio; RNA Seq	GSM5538908		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538908	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_4_1.fq.gz SP_6W_4_2.fq.gz	fastq fastq	19724695800.0	65748986.0	GSM5538908 r1	0:150 1:150	A:6112379944;C:3229510802;G:3753824243;T:6628648367;N:332444	150	150		6112379944	3229510802	3753824243	6628648367	332444	SRX11923654	SRS9937164	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.76792	0.76848	0.22326	0.22438	0.8747	0.87732	0.68095	0.68566	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65790	65790	SRR15626590	SRX11923653	SRS9937163	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 3	GSM5538907		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538907	GSM5538907: SP 6W 3; Danio rerio; RNA Seq	GSM5538907		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538907	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_3_1.fq.gz SP_6W_3_2.fq.gz	fastq fastq	22917868200.0	76392894.0	GSM5538907 r1	0:150 1:150	A:6801610029;C:4223124283;G:4702480567;T:7190055774;N:597547	150	150		6801610029	4223124283	4702480567	7190055774	597547	SRX11923653	SRS9937163	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.57129	0.57016	0.16002	0.16225	0.91634	0.91729	0.59641	0.5943	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65791	65791	SRR15626589	SRX11923652	SRS9937161	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 2	GSM5538906		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538906	GSM5538906: SP 6W 2; Danio rerio; RNA Seq	GSM5538906		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538906	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_2_1.fq.gz SP_6W_2_2.fq.gz	fastq fastq	24852190200.0	82840634.0	GSM5538906 r1	0:150 1:150	A:7405379331;C:4430315593;G:5004669375;T:8011250066;N:575835	150	150		7405379331	4430315593	5004669375	8011250066	575835	SRX11923652	SRS9937161	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.62502	0.61952	0.13619	0.13651	0.90433	0.90569	0.6187	0.64354	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65792	65792	SRR15626588	SRX11923651	SRS9937162	SRP334274	PRJNA758087	Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury	GSE182869	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Bulk RNA Seq samples of ISNs from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. Sequencing libraries N=5 6 were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions NEB. We mapped about 50 60 million sequence reads per sample to the zebrafish genome and identified 39 714 transcripts in the zebrafish intraspinal serotonergic neurons. Our study represents the detailed analysis of transcriptomes of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments post spinal cord injury. Overall design: Bulk RNA Seq samples of intraspinal serotonergic neurons from the injury area and residual segments respectively were FAC sorted from Tgtph2:GFP line. Total RNA was extracted and cDNA libraries N=5 6 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		SP 6W 1	GSM5538905		source name:spinal cord\|strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	SP 6W 1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:Tgtph2:GFP\|tissue:spinal cord segment in the injury site\|cell type:serot1rgic neuron\|disease state:6 8 xxx post injury	GSM5538905	GSM5538905: SP 6W 1; Danio rerio; RNA Seq	GSM5538905		1	Spinal cord tissue of the injury area and residual segments were dissected out. Intraspinal serotonin neurons were isolated from Tgtph2:GFP line by FAC sorting flash frozen on dry ice. Total RNA was isolated using SMART SeqTM v4 UltraTM Low Input RNA Kit for Sequencing Clontech. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538905	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334274		loader:fastq load.py	SP_6W_1_1.fq.gz SP_6W_1_2.fq.gz	fastq fastq	24620126100.0	82067087.0	GSM5538905 r1	0:150 1:150	A:7560561068;C:3977462807;G:4611993481;T:8469791572;N:317172	150	150		7560561068	3977462807	4611993481	8469791572	317172	SRX11923651	SRS9937162	SRA1284222	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.82479	0.8193	0.2795	0.27737	0.83011	0.83374	0.58026	0.57852	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc	single_cell_plate	smartseq	China	2021-08-26	Undetermined	Undetermined	Spinal Cord	Nervous System
65793	65793	SRR15626575	SRX11923642	SRS9937160	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 C5	GSM5538904		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	W6 C5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	GSM5538904	GSM5538904: W6 C5; Danio rerio; RNA Seq	GSM5538904		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538904	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_C5_1.fq.gz W6_C5_2.fq.gz	fastq fastq	11548053600.0	38493512.0	GSM5538904 r1	0:150 1:150	A:3284639772;C:2417614008;G:2424125351;T:3421247186;N:427283	150	150		3284639772	2417614008	2424125351	3421247186	427283	SRX11923642	SRS9937160	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.92424	0.91753	0.09206	0.08921	0.73817	0.75006	0.48669	0.46123	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65794	65794	SRR15626574	SRX11923641	SRS9937158	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 C3	GSM5538903		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	W6 C3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	GSM5538903	GSM5538903: W6 C3; Danio rerio; RNA Seq	GSM5538903		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538903	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_C3_1.fq.gz W6_C3_2.fq.gz	fastq fastq	8675036411.0	29294039.0	GSM5538903 r1		A:2490417531;C:1754549667;G:1762976045;T:2666940038;N:153130				2490417531	1754549667	1762976045	2666940038	153130	SRX11923641	SRS9937158	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.77214	0.76518	0.16042	0.15604	0.72425	0.74251	0.47844	0.47263	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65795	65795	SRR15626573	SRX11923640	SRS9937159	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 C2	GSM5538902		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	W6 C2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	GSM5538902	GSM5538902: W6 C2; Danio rerio; RNA Seq	GSM5538902		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538902	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_C2_1.fq.gz W6_C2_2.fq.gz	fastq fastq	10539241978.0	35799607.0	GSM5538902 r1		A:2981919265;C:2108326349;G:2140188676;T:3307713377;N:1094311				2981919265	2108326349	2140188676	3307713377	1094311	SRX11923640	SRS9937159	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.79298	0.77869	0.15756	0.14594	0.71504	0.73527	0.52219	0.3777	126	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65796	65796	SRR15626572	SRX11923639	SRS9937157	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 C1	GSM5538901		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	W6 C1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:6 xxx post injury	GSM5538901	GSM5538901: W6 C1; Danio rerio; RNA Seq	GSM5538901		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538901	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_C1_1.fq.gz W6_C1_2.fq.gz	fastq fastq	10943049099.0	37073140.0	GSM5538901 r1		A:3130283377;C:2198486300;G:2220073292;T:3393075128;N:1131002				3130283377	2198486300	2220073292	3393075128	1131002	SRX11923639	SRS9937157	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.80382	0.80796	0.16342	0.16071	0.72275	0.73456	0.49635	0.49821	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65797	65797	SRR15626571	SRX11923638	SRS9937156	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 R5	GSM5538900		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	W6 R5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	GSM5538900	GSM5538900: W6 R5; Danio rerio; RNA Seq	GSM5538900		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538900	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_R5_1.fq.gz W6_R5_2.fq.gz	fastq fastq	12204896100.0	40682987.0	GSM5538900 r1	0:150 1:150	A:3461249396;C:2529425680;G:2571904738;T:3640345896;N:1970390	150	150		3461249396	2529425680	2571904738	3640345896	1970390	SRX11923638	SRS9937156	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.91134	0.91584	0.10821	0.10746	0.73588	0.75207	0.52657	0.48765	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65798	65798	SRR15626570	SRX11923637	SRS9937155	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 R4	GSM5538899		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	W6 R4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	GSM5538899	GSM5538899: W6 R4; Danio rerio; RNA Seq	GSM5538899		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538899	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_R4_1.fq.gz W6_R4_2.fq.gz	fastq fastq	11563962300.0	38546541.0	GSM5538899 r1	0:150 1:150	A:3303789178;C:2399710240;G:2415791330;T:3443551642;N:1119910	150	150		3303789178	2399710240	2415791330	3443551642	1119910	SRX11923637	SRS9937155	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.91143	0.90985	0.11486	0.11393	0.73825	0.74533	0.54532	0.52817	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65799	65799	SRR15626569	SRX11923636	SRS9937154	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 R3	GSM5538898		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	W6 R3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	GSM5538898	GSM5538898: W6 R3; Danio rerio; RNA Seq	GSM5538898		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538898	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_R3_1.fq.gz W6_R3_2.fq.gz	fastq fastq	10585954542.0	35816604.0	GSM5538898 r1		A:3037575766;C:2127628123;G:2139476709;T:3281099271;N:174673				3037575766	2127628123	2139476709	3281099271	174673	SRX11923636	SRS9937154	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.85058	0.85296	0.1621	0.15714	0.71713	0.73582	0.52255	0.50069	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65800	65800	SRR15626568	SRX11923635	SRS9937153	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 R2	GSM5538897		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	W6 R2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	GSM5538897	GSM5538897: W6 R2; Danio rerio; RNA Seq	GSM5538897		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538897	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_R2_1.fq.gz W6_R2_2.fq.gz	fastq fastq	10669861075.0	36260298.0	GSM5538897 r1		A:3008779806;C:2132058614;G:2164237979;T:3363597660;N:1187016				3008779806	2132058614	2164237979	3363597660	1187016	SRX11923635	SRS9937153	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.80233	0.78844	0.14557	0.1354	0.7179	0.73914	0.50279	0.38358	150	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65801	65801	SRR15626567	SRX11923634	SRS9937152	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W6 R1	GSM5538896		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	W6 R1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:6 xxx post injury	GSM5538896	GSM5538896: W6 R1; Danio rerio; RNA Seq	GSM5538896		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538896	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W6_R1_1.fq.gz W6_R1_2.fq.gz	fastq fastq	8919305763.0	30118529.0	GSM5538896 r1		A:2544200186;C:1819461355;G:1834522593;T:2720239204;N:882425				2544200186	1819461355	1834522593	2720239204	882425	SRX11923634	SRS9937152	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.81775	0.81798	0.17053	0.16924	0.7161	0.72971	0.50177	0.49561	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65802	65802	SRR15626566	SRX11923633	SRS9937151	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C5	GSM5538895		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538895	GSM5538895: W4 C5; Danio rerio; RNA Seq	GSM5538895		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538895	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_C5_1.fq.gz W4_C5_2.fq.gz	fastq fastq	11543122500.0	38477075.0	GSM5538895 r1	0:150 1:150	A:3264584729;C:2405081333;G:2441204011;T:3430418662;N:1833765	150	150		3264584729	2405081333	2441204011	3430418662	1833765	SRX11923633	SRS9937151	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.91535	0.91481	0.10079	0.09867	0.73671	0.75333	0.497	0.47606	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65803	65803	SRR15626565	SRX11923632	SRS9937150	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C4	GSM5538894		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538894	GSM5538894: W4 C4; Danio rerio; RNA Seq	GSM5538894		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538894	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_C4_1.fq.gz W4_C4_2.fq.gz	fastq fastq	12129480900.0	40431603.0	GSM5538894 r1	0:150 1:150	A:3451519288;C:2515952240;G:2531389661;T:3629453781;N:1165930	150	150		3451519288	2515952240	2531389661	3629453781	1165930	SRX11923632	SRS9937150	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.90598	0.90619	0.11287	0.10949	0.74184	0.75049	0.52714	0.51794	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65804	65804	SRR15626564	SRX11923631	SRS9937149	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C3	GSM5538893		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538893	GSM5538893: W4 C3; Danio rerio; RNA Seq	GSM5538893		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538893	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_C3_1.fq.gz W4_C3_2.fq.gz	fastq fastq	14082618084.0	47123575.0	GSM5538893 r1		A:4015557919;C:3022962754;G:2997180467;T:4041325245;N:5591699				4015557919	3022962754	2997180467	4041325245	5591699	SRX11923631	SRS9937149	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.92908	0.92957	0.15754	0.15803	0.6929	0.70116	0.47235	0.46006	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65805	65805	SRR15626563	SRX11923630	SRS9937148	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C2	GSM5538892		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538892	GSM5538892: W4 C2; Danio rerio; RNA Seq	GSM5538892		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538892	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_C2_1.fq.gz W4_C2_2.fq.gz	fastq fastq	9869014911.0	33378223.0	GSM5538892 r1		A:2804174507;C:2004352577;G:2027844843;T:3031342717;N:1300267				2804174507	2004352577	2027844843	3031342717	1300267	SRX11923630	SRS9937148	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.74408	0.76084	0.15302	0.15477	0.71871	0.72863	0.41139	0.49828	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65806	65806	SRR15626562	SRX11923629	SRS9937147	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C1	GSM5538891		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538891	GSM5538891: W4 C1; Danio rerio; RNA Seq	GSM5538891		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538891	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_C1_1.fq.gz W4_C1_2.fq.gz	fastq fastq	10687932882.0	36203087.0	GSM5538891 r1		A:3008283529;C:2182572792;G:2209894531;T:3285549998;N:1632032				3008283529	2182572792	2209894531	3285549998	1632032	SRX11923629	SRS9937147	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.78654	0.7865	0.12675	0.12286	0.71973	0.73154	0.48571	0.48208	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65807	65807	SRR15626561	SRX11923628	SRS9937146	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 R5	GSM5538890		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	W4 R5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	GSM5538890	GSM5538890: W4 R5; Danio rerio; RNA Seq	GSM5538890		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538890	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_R5_1.fq.gz W4_R5_2.fq.gz	fastq fastq	10826625600.0	36088752.0	GSM5538890 r1	0:150 1:150	A:3070709719;C:2256203149;G:2290582547;T:3207400991;N:1729194	150	150		3070709719	2256203149	2290582547	3207400991	1729194	SRX11923628	SRS9937146	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.92731	0.92152	0.09349	0.09234	0.74298	0.75749	0.51393	0.5062	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65808	65808	SRR15626560	SRX11923627	SRS9937144	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 R4	GSM5538889		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	W4 R4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	GSM5538889	GSM5538889: W4 R4; Danio rerio; RNA Seq	GSM5538889		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538889	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_R4_1.fq.gz W4_R4_2.fq.gz	fastq fastq	12376562700.0	41255209.0	GSM5538889 r1	0:150 1:150	A:3541278294;C:2530972782;G:2556584213;T:3745659123;N:2068288	150	150		3541278294	2530972782	2556584213	3745659123	2068288	SRX11923627	SRS9937144	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.89512	0.89467	0.10934	0.10598	0.7501	0.76045	0.55625	0.53279	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65809	65809	SRR15626559	SRX11923626	SRS9937145	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 R3	GSM5538888		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	W4 R3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	GSM5538888	GSM5538888: W4 R3; Danio rerio; RNA Seq	GSM5538888		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538888	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_R3_1.fq.gz W4_R3_2.fq.gz	fastq fastq	12994033001.0	43618576.0	GSM5538888 r1		A:3734612575;C:2723842641;G:2695083832;T:3835271719;N:5222234				3734612575	2723842641	2695083832	3835271719	5222234	SRX11923626	SRS9937145	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.92675	0.92704	0.17531	0.17471	0.71407	0.72421	0.49948	0.49784	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65810	65810	SRR15626558	SRX11923625	SRS9937143	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 R2	GSM5538887		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	W4 R2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	GSM5538887	GSM5538887: W4 R2; Danio rerio; RNA Seq	GSM5538887		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538887	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_R2_1.fq.gz W4_R2_2.fq.gz	fastq fastq	9939535918.0	33661519.0	GSM5538887 r1		A:2798350929;C:2035721017;G:2056764740;T:3047330104;N:1369128				2798350929	2035721017	2056764740	3047330104	1369128	SRX11923625	SRS9937143	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.83192	0.82813	0.14852	0.14323	0.70822	0.7247	0.5042	0.39639	150	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65811	65811	SRR15626557	SRX11923624	SRS9937142	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 R1	GSM5538886		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	W4 R1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:4 xxx post injury	GSM5538886	GSM5538886: W4 R1; Danio rerio; RNA Seq	GSM5538886		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538886	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W4_R1_1.fq.gz W4_R1_2.fq.gz	fastq fastq	11296616614.0	38212724.0	GSM5538886 r1		A:3243016820;C:2270852137;G:2299184572;T:3481964410;N:1598675				3243016820	2270852137	2299184572	3481964410	1598675	SRX11923624	SRS9937142	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.82944	0.83777	0.17869	0.17723	0.71887	0.72855	0.55802	0.54964	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65812	65812	SRR15626556	SRX11923623	SRS9937141	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 C5	GSM5538885		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	W2 C5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	GSM5538885	GSM5538885: W2 C5; Danio rerio; RNA Seq	GSM5538885		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538885	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_C5_1.fq.gz W2_C5_2.fq.gz	fastq fastq	12070135500.0	40233785.0	GSM5538885 r1	0:150 1:150	A:3401996219;C:2534578869;G:2548303668;T:3583247357;N:2009387	150	150		3401996219	2534578869	2548303668	3583247357	2009387	SRX11923623	SRS9937141	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.9072	0.90232	0.11716	0.11618	0.72636	0.73685	0.5018	0.49535	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65813	65813	SRR15626555	SRX11923622	SRS9937139	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 C4	GSM5538884		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	W2 C4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	GSM5538884	GSM5538884: W2 C4; Danio rerio; RNA Seq	GSM5538884		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538884	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_C4_1.fq.gz W2_C4_2.fq.gz	fastq fastq	10594271400.0	35314238.0	GSM5538884 r1	0:150 1:150	A:2987614251;C:2191740653;G:2212201491;T:3200908482;N:1806523	150	150		2987614251	2191740653	2212201491	3200908482	1806523	SRX11923622	SRS9937139	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.91565	0.91107	0.10017	0.09553	0.74253	0.7543	0.57884	0.57058	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65814	65814	SRR15626554	SRX11923621	SRS9937140	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 C3	GSM5538883		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	W2 C3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	GSM5538883	GSM5538883: W2 C3; Danio rerio; RNA Seq	GSM5538883		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538883	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_C3_1.fq.gz W2_C3_2.fq.gz	fastq fastq	13355624941.0	44841516.0	GSM5538883 r1		A:3801123201;C:2832441023;G:2806117424;T:3910715830;N:5227463				3801123201	2832441023	2806117424	3910715830	5227463	SRX11923621	SRS9937140	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.93011	0.93014	0.14881	0.1487	0.70934	0.72023	0.50145	0.49419	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65815	65815	SRR15626553	SRX11923620	SRS9937138	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 C2	GSM5538882		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	W2 C2	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	GSM5538882	GSM5538882: W2 C2; Danio rerio; RNA Seq	GSM5538882		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538882	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_C2_1.fq.gz W2_C2_2.fq.gz	fastq fastq	9734471313.0	32968420.0	GSM5538882 r1		A:2724735296;C:2009064775;G:2033048131;T:2966320646;N:1302465				2724735296	2009064775	2033048131	2966320646	1302465	SRX11923620	SRS9937138	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.7713	0.78947	0.11743	0.11671	0.71741	0.72736	0.49335	0.4863	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65816	65816	SRR15626552	SRX11923619	SRS9937137	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 C1	GSM5538881		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	W2 C1	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:2 xxx post injury	GSM5538881	GSM5538881: W2 C1; Danio rerio; RNA Seq	GSM5538881		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538881	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_C1_1.fq.gz W2_C1_2.fq.gz	fastq fastq	9082436552.0	30805602.0	GSM5538881 r1		A:2559732121;C:1843621019;G:1872765497;T:2804939348;N:1378567				2559732121	1843621019	1872765497	2804939348	1378567	SRX11923619	SRS9937137	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.76943	0.78719	0.13099	0.13069	0.7259	0.73679	0.51491	0.39397	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65817	65817	SRR15626551	SRX11923618	SRS9937136	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 R5	GSM5538880		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	W2 R5	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	GSM5538880	GSM5538880: W2 R5; Danio rerio; RNA Seq	GSM5538880		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538880	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_R5_1.fq.gz W2_R5_2.fq.gz	fastq fastq	13733467500.0	45778225.0	GSM5538880 r1	0:150 1:150	A:3893031167;C:2866552637;G:2882457798;T:4090098547;N:1327351	150	150		3893031167	2866552637	2882457798	4090098547	1327351	SRX11923618	SRS9937136	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.92215	0.91781	0.10294	0.10091	0.73434	0.74164	0.50738	0.50448	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65818	65818	SRR15626550	SRX11923617	SRS9937135	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 R4	GSM5538879		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	W2 R4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	GSM5538879	GSM5538879: W2 R4; Danio rerio; RNA Seq	GSM5538879		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538879	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_R4_1.fq.gz W2_R4_2.fq.gz	fastq fastq	11955951600.0	39853172.0	GSM5538879 r1	0:150 1:150	A:3384460570;C:2474116532;G:2513217291;T:3582811941;N:1345266	150	150		3384460570	2474116532	2513217291	3582811941	1345266	SRX11923617	SRS9937135	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.9114	0.90987	0.09871	0.09717	0.73675	0.75148	0.50932	0.50986	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System
65819	65819	SRR15626549	SRX11923616	SRS9937134	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W2 R3	GSM5538878		source name:spinal cord\|strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	W2 R3	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment rostral to the injury site\|disease state:2 xxx post injury	GSM5538878	GSM5538878: W2 R3; Danio rerio; RNA Seq	GSM5538878		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538878	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP334272		loader:fastq load.py	W2_R3_1.fq.gz W2_R3_2.fq.gz	fastq fastq	11388586527.0	38223361.0	GSM5538878 r1		A:3239034105;C:2424523990;G:2400765702;T:3319676527;N:4586203				3239034105	2424523990	2400765702	3319676527	4586203	SRX11923616	SRS9937134	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.93006	0.93152	0.13219	0.1324	0.71202	0.72316	0.46964	0.46882	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System

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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");;