metadata: run_metadata: 73 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue

73 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Tail"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
52243	52243	SRR9050632	SRX5827023	SRS4754837	SRP198298	PRJNA542704	Thyroid hormone regulates distinct paths to maturation in pigment cell lineages	GSE131136	Transcriptome Analysis	Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.	pubmed:31140974;pubmed:33933422	Neural crest derived cells from 5 dpf euthyroid zebrafish tails	GSM3764579	tissue:sox10:Cre+ cells from 5 dpf zebrafish tail tissue\|cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.\|treatment:Untreated	Neural crest derived cells from 5 dpf euthyroid zebrafish tails	Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.	sox10:Cre+ cells from 5 dpf zebrafish tail tissue	Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.	Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.	cell type:2154 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from tails of 5 dpf zebrafish.\|treatment:Untreated	GSM3764579	GSM3764579: Neural crest derived cells from 5 dpf euthyroid zebrafish tails; Danio rerio; RNA Seq	GSM3764579	1	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP198298	dangling references:treat as unmapped	5dpf_possorted_genome_bam.bam	10X Genomics bam file	6566978892.0	115210156.0	GSM3764579 r1	0:57	A:1984051591;C:1302406550;G:1514564296;T:1762601545;N:3354910	57				1984051591	1302406550	1514564296	1762601545	3354910	SRX5827023	SRS4754837	SRA886020	GEO	Biology, University of Virginia	1	0.9291		0.194		0.81466		0.53116		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-05-13	Larval	Larval	Tail	Multi-system
56820	56820	SRR15414667	SRX11716797	SRS9747215	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	UI 2DG	GSM5513441	tissue:Developing embryonic zebrafish tail\|strain:TAB 5\|embryo age:3 dpf mM 2 deoxyglucose	UI 2DG	Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics	Developing embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics		strain:TAB 5\|embryo age:3 dpf mM 2 deoxyglucose	GSM5513441	GSM5513441: UI 2DG; Danio rerio; RNA Seq	GSM5513441	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics	GEO Accession:GSM5513441	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	assembly:Danio Rerio 11\|intentional duplicate	UI_2DG.bam	10X Genomics bam file	7617244817.0	83705987.0	GSM5513441 r1	0:91	A:2234691645;C:1513876602;G:1889440050;T:1970597369;N:8639151	91				2234691645	1513876602	1889440050	1970597369	8639151	SRX11716797	SRS9747215	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.93814		0.15677		0.8254		0.52455		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-11	Larval	Larval	Tail	Multi-system
56821	56821	SRR15414666	SRX11716796	SRS9747214	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	UI ctrl	GSM5513440	tissue:Regenerating embryonic zebrafish tail\|strain:TAB 5\|embryo age:3 dpf	UI ctrl	Binary Base Call BCL files generated from an Illumina 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics Genome build: Danio Rerio 11 Supplementary files format and content: clouple files are provided which can be visiualized with the Loupe Cell Browser 10x Genomics	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics		strain:TAB 5\|embryo age:3 dpf	GSM5513440	GSM5513440: UI ctrl; Danio rerio; RNA Seq	GSM5513440	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries was generatated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics	GEO Accession:GSM5513440	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	assembly:Danio Rerio 11\|intentional duplicate	UI_ctrl.bam	10X Genomics bam file	8002896265.0	87943915.0	GSM5513440 r1	0:91	A:2325005630;C:1613869115;G:2033844364;T:2021144325;N:9032831	91				2325005630	1613869115	2033844364	2021144325	9032831	SRX11716796	SRS9747214	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.93599		0.15189		0.83603		0.50802		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-11	Larval	Larval	Tail	Multi-system
56822	56822	SRR11107235	SRX7744906	SRS6164695	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	48hpa 2DG	GSM4319213	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf mM 2 deoxyglucose\|time point:48hpa	48hpa 2DG	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf mM 2 deoxyglucose\|time point:48hpa	GSM4319213	GSM4319213: 48hpa 2DG; Danio rerio; RNA Seq	GSM4319213	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	48hpa_2DG.bam	10X Genomics bam file	6786532025.0	74577275.0	GSM4319213 r1	0:91	A:1972992538;C:1368168542;G:1707658855;T:1729990330;N:7721760	91				1972992538	1368168542	1707658855	1729990330	7721760	SRX7744906	SRS6164695	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.9456		0.16065		0.80852		0.56712		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56823	56823	SRR11107234	SRX7744905	SRS6165316	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	48hpa ctrl	GSM4319212	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf point:48hpa	48hpa ctrl	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:5 dpf point:48hpa	GSM4319212	GSM4319212: 48hpa ctrl; Danio rerio; RNA Seq	GSM4319212	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319212	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	48hpa_ctrl.bam	10X Genomics bam file	6315141924.0	69397164.0	GSM4319212 r1	0:91	A:1820671652;C:1274680094;G:1600555332;T:1612090454;N:7144392	91				1820671652	1274680094	1600555332	1612090454	7144392	SRX7744905	SRS6165316	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.94831		0.155		0.80866		0.5428		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56824	56824	SRR11107233	SRX7744904	SRS6165317	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	24hpa 2DG	GSM4319211	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf mM 2 deoxyglucose\|time point:24hpa	24hpa 2DG	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf mM 2 deoxyglucose\|time point:24hpa	GSM4319211	GSM4319211: 24hpa 2DG; Danio rerio; RNA Seq	GSM4319211	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319211	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	24hpa_2DG.bam	10X Genomics bam file	4751770569.0	52217259.0	GSM4319211 r1	0:91	A:1367937805;C:991264209;G:1237114736;T:1153230321;N:2223498	91				1367937805	991264209	1237114736	1153230321	2223498	SRX7744904	SRS6165317	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.8338		0.14372		0.82108		0.57161		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
56825	56825	SRR11107232	SRX7744903	SRS6164694	SRP249927	PRJNA607316	The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration	GSE145497	Transcriptome Analysis	Throughout their lifetime fish maintain a high capacity for regenerating complex xxx post injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio which serves as an ideal model of appendage regeneration due to its easy manipulation relatively simple mixture of cell types and superior imaging properties. Regeneration of the embryonic zebrafish tail requires development of a blastema a mass of dedifferentiated cells capable of replacing lost tissue a crucial step in all known examples of appendage regeneration. Using this model we show that tail amputation triggers an obligate metabolic shift to promote glucose metabolism during early regeneration similar to the Warburg effect observed in tumor forming cells. Inhibition of glucose metabolism did not affect the overall health of the embryo but completely blocked the fin from regenerating post amputation due to the failure to form a functional blastema. We performed a time series of single cell RNA sequencing on regenerating tails with and without xxx of glucose metabolism. We demonstrated that metabolic reprogramming is required for sustained TGF ß signaling and blocking glucose metabolism largely mimicked inhibition of TGF ß receptors both resulting in an aberrant blastema. Finally we showed using genetic ablation of three possible metabolic pathways for glucose that metabolic reprogramming is required to provide glucose specifically to the hexosamine biosynthetic pathway while neither glycolysis nor the pentose phosphate pathway were necessary for regeneration. Overall design: Single cell RNAseq data was generated from uninjured or regenerating embryonic zebrafish tails at 24 and 48 hours post amputation with and without xxx deoxyglucose. Please note that the UI ctrl.cloupe is a single sample from uninjured untreated embryo tails and the ctrl cloupe.cloupe is an aggregate file of all non 2DG treated samples UI ctrl 24hpa ctrl and 48hpa ctrl.	pubmed:34518542	24hpa ctrl	GSM4319210	source name:Regenerating embryonic zebrafish tail\|strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf point:24hpa	24hpa ctrl	Binary Base Call BCL files generated from an Illumina NextSeq 550 sequencer and converted to FASTQ files with Cell Ranger Version 3.0.2 10x Genomics. Cell Ranger Version 3.0.2. was used to demultiplex for barcode processing for single cell gene counts and aggregating files. Further analyses of the samples was performed using Loupe Cell Browser 10x Genomics. Genome build: Danio Rerio 11 danRer11 GRCz11 Supplementary files format and content: cloupe files are provided which can be visualized with the Loupe Cell Browser 10x Genomics. Supplementary files format and content: hd5 files.	Regenerating embryonic zebrafish tail		Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.		strain:TAB 5\|tissue:Regenerating embryonic tail\|embryo age:4 dpf point:24hpa	GSM4319210	GSM4319210: 24hpa ctrl; Danio rerio; RNA Seq	GSM4319210	1	Regenerating tails were amputated and dissociated to single cells using trypsin and collagenase. cDNA libraries were generated with Chromium Controller and Chromium Single Cell three prime GEM Library and Gel Bead Kit V3 10x Genomics.	GEO Accession:GSM4319210	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP249927	intentional duplicate	24hpa_ctrl.bam	10X Genomics bam file	5461996085.0	60021935.0	GSM4319210 r1	0:91	A:1578516213;C:1146696708;G:1390321964;T:1344258467;N:2202733	91				1578516213	1146696708	1390321964	1344258467	2202733	SRX7744903	SRS6164694	SRA1044429	GEO	National Human Genome Research Institute, National Institutes of Health	1	0.83781		0.14102		0.81264		0.58676		91		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2020-02-18	Larval	Larval	Tail	Multi-system
63865	63865	SRR14143478	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.		Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S1 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S1 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S1 L003 R2 001.fastq.gz			31286394882.0	246349566.0	GSM5226215 r1	0:8 1:28 2:91	A:8483875403;C:6562544452;G:7703313223;T:8535328683;N:1333121	8	28	91		8483875403	6562544452	7703313223	8535328683	1333121	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94915		0.12419		0.79411		0.48155		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63866	63866	SRR14143479	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.		Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S2 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S2 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S2 L003 R2 001.fastq.gz	WT_tailbud_S2_L003_I1_001.fastq.gz WT_tailbud_S2_L003_R1_001.fastq.gz WT_tailbud_S2_L003_R2_001.fastq.gz	fastq fastq fastq	34222167268.0	269465884.0	GSM5226215 r2	0:8 1:28 2:91	A:10380791879;C:7173180527;G:7598116520;T:9068620061;N:1458281	8	28	91		10380791879	7173180527	7598116520	9068620061	1458281	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94862		0.1236		0.79322		0.50153		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63867	63867	SRR14143480	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.		Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S3 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S3 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S3 L003 R2 001.fastq.gz	WT_tailbud_S3_L003_I1_001.fastq.gz WT_tailbud_S3_L003_R1_001.fastq.gz WT_tailbud_S3_L003_R2_001.fastq.gz	fastq fastq fastq	33676411438.0	265168594.0	GSM5226215 r3	0:8 1:28 2:91	A:9145545141;C:7581198882;G:7228819079;T:9719412772;N:1435564	8	28	91		9145545141	7581198882	7228819079	9719412772	1435564	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94728		0.12372		0.79366		0.49386		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63868	63868	SRR14143481	SRX10512841	SRS8636598	SRP313475	PRJNA719789	scRNA seq of tailbud development in zebrafish	GSE171482	Other	We have performed single cell RNA seq of whole tailbuds in WT zebrafish at 16 hpf. Overall design: Single cells were captured via 10X Chromium platform at 16 hpf from whole tailbuds.		Tailbud single cells at 16 hpf	GSM5226215	source name:Dissociated tailbuds from 30 hpf 16 hpf embryos\|transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	Tailbud single cells at 16 hpf	FASTQs were mapped to zebrafish genome and counts were calculated using CellRanger. Further processing was performed using Seurat v3 in R Low quality cells and doublets were excluded based on thresholds for number of genes detected >1500; <4000 Unhealthy cells were excluded based on threshold for percent of mitochondrial genes detected <4% Genome build: GRCz11 Supplementary files format and content: .csv file contains counts matrix for each cell that met quality thresholds	Dissociated tailbuds from 30 hpf 16 hpf embryos		Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3		transgenic:AB wildtypes\|age:16 hpf embryo\|tissue:dissociated tailbuds	GSM5226215	GSM5226215: Tailbud single cells at 16 hpf; Danio rerio; RNA Seq	GSM5226215	1	Tailbuds were manually dissected and then dissociated using collagenase P and trypsin Libraries were constructed using a 10X chromium platofrm according to standard 10X Genomics protocols. Linraries used 10X Chromiium chemistry v2 except Sample 7 which used chemistry v3	GEO Accession:GSM5226215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP313475	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=WT tailbud S4 L003 I1 001.fastq.gz read2PairFiles=WT tailbud S4 L003 R1 001.fastq.gz read3PairFiles=WT tailbud S4 L003 R2 001.fastq.gz	WT_tailbud_S4_L003_I1_001.fastq.gz WT_tailbud_S4_L003_R1_001.fastq.gz WT_tailbud_S4_L003_R2_001.fastq.gz	fastq fastq fastq	30944524598.0	243657674.0	GSM5226215 r4	0:8 1:28 2:91	A:8382983101;C:6979019830;G:7383731031;T:8197465285;N:1325351	8	28	91		8382983101	6979019830	7383731031	8197465285	1325351	SRX10512841	SRS8636598	SRA1215249	GEO	Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine	1	0.94927		0.12443		0.79316		0.48307		91		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-04-05	Segmentation	Embryo	Tail	Multi-system
63887	63887	SRR14202114	SRX10569027	SRS8675160	SRP314271	PRJNA720970	Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos	GSE171822	Transcriptome Analysis	We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.	pubmed:36693371	RNA seq the other ECs	GSM5235246	source name:resected tails posterior to the yolk end\|strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:other ECs TagRFP /EGFP+	RNA seq the other ECs	The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample.	resected tails posterior to the yolk end		Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.		strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:other ECs TagRFP /EGFP+	GSM5235246	GSM5235246: RNA seq the other ECs; Danio rerio; RNA Seq	GSM5235246	1	Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.	GEO Accession:GSM5235246	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP314271	loader:fastq load.py\|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP RFP I1.fastq.gz read2PairFiles=ZebEmb GFP RFP I2.fastq.gz read3PairFiles=ZebEmb GFP RFP R1.fastq.gz read4PairFiles=ZebEmb GFP RFP R2.fastq.gz	ZebEmb_GFP_RFP_I1.fastq.gz ZebEmb_GFP_RFP_I2.fastq.gz ZebEmb_GFP_RFP_R1.fastq.gz ZebEmb_GFP_RFP_R2.fastq.gz	fastq fastq fastq fastq	46144044078.0	334377131.0	GSM5235246 r1	0:10 1:10 2:28 3:90	A:12365801825;C:10786766050;G:11098071597;T:11890763395;N:2641211	10	10	28	90	12365801825	10786766050	11098071597	11890763395	2641211	SRX10569027	SRS8675160	SRA1217192	GEO	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.93604		0.14513		0.79038		0.50811		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2021-04-09	Hatching	Embryo	Tail	Multi-system
63888	63888	SRR14202113	SRX10569026	SRS8675161	SRP314271	PRJNA720970	Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos	GSE171822	Transcriptome Analysis	We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.	pubmed:36693371	RNA seq isl1 derived ECs	GSM5235245	source name:resected tails posterior to the yolk end\|strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	RNA seq isl1 derived ECs	The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample.	resected tails posterior to the yolk end		Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.		strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	GSM5235245	GSM5235245: RNA seq isl1 derived ECs; Danio rerio; RNA Seq	GSM5235245	1	Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.	GEO Accession:GSM5235245	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP314271	loader:fastq load.py\|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP I1.fastq.gz read2PairFiles=ZebEmb GFP I2.fastq.gz read3PairFiles=ZebEmb GFP R1.fastq.gz read4PairFiles=ZebEmb GFP R2.fastq.gz	ZebEmb_GFP_I1.fastq.gz ZebEmb_GFP_I2.fastq.gz ZebEmb_GFP_R1.fastq.gz ZebEmb_GFP_R2.fastq.gz	fastq fastq fastq fastq	53036547366.0	384322807.0	GSM5235245 r1	0:10 1:10 2:28 3:90	A:14610188978;C:12169986421;G:12283689207;T:13969658178;N:3024582	10	10	28	90	14610188978	12169986421	12283689207	13969658178	3024582	SRX10569026	SRS8675161	SRA1217192	GEO	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.94469		0.10454		0.79133		0.51214		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Japan	2021-04-09	Hatching	Embryo	Tail	Multi-system
64263	64263	SRR14428602	SRX10779739	SRS8866172	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 4	GSM5282506	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282506	GSM5282506: scRNA seq of notum 1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282506	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282506	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_MG2_S40_L006_R1_001.fastq.gz WNT_MG2_S40_L006_R2_001.fastq.gz	fastq fastq	59309016800.0	296545084.0	GSM5282506 r1	0:100 1:100	A:13101652467;C:9053865386;G:9914199388;T:27226829088;N:12470471	100	100			13101652467	9053865386	9914199388	27226829088	12470471	SRX10779739	SRS8866172	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00907	0.91374	0.00232	0.07221	0.99293	0.82822	0.5	0.50749	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64264	64264	SRR14428601	SRX10779738	SRS8866171	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 3	GSM5282505	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282505	GSM5282505: scRNA seq of notum 1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282505	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282505	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_MG1_S39_L005_R1_001.fastq.gz WNT_MG1_S39_L005_R2_001.fastq.gz	fastq fastq	75003307800.0	375016539.0	GSM5282505 r1	0:100 1:100	A:17011122660;C:12505646501;G:12322737410;T:33144126985;N:19674244	100	100			17011122660	12505646501	12322737410	33144126985	19674244	SRX10779738	SRS8866171	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.0068	0.94221	0.00175	0.08258	0.99608	0.82473	0.49289	0.52202	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64265	64265	SRR14428600	SRX10779737	SRS8866170	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 2	GSM5282504	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282504	GSM5282504: scRNA seq of notum 1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282504	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282504	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_DJ2_S42_L008_R1_001.fastq.gz WNT_DJ2_S42_L008_R2_001.fastq.gz	fastq fastq	73921649200.0	369608246.0	GSM5282504 r1	0:100 1:100	A:16691509262;C:12147679273;G:12179457462;T:32881202116;N:21801087	100	100			16691509262	12147679273	12179457462	32881202116	21801087	SRX10779737	SRS8866170	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00683	0.92595	0.00109	0.08047	0.99531	0.82558	0.5017	0.48675	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64266	64266	SRR14428599	SRX10779736	SRS8866169	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of notum 1 treatment embryo replicate 1	GSM5282503	tissue:tail\|treatment:notum 1	scRNA seq of notum 1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:notum 1	GSM5282503	GSM5282503: scRNA seq of notum 1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282503	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282503	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543		WNT_DJ1_S41_L007_R1_001.fastq.gz WNT_DJ1_S41_L007_R2_001.fastq.gz	fastq fastq	72873756000.0	364368780.0	GSM5282503 r1	0:100 1:100	A:16621508845;C:12254073814;G:11510875104;T:32473791832;N:13506405	100	100			16621508845	12254073814	11510875104	32473791832	13506405	SRX10779736	SRS8866169	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	2	0.00358	0.94302	0.0008	0.08218	0.99803	0.82181	0.50485	0.51251	100	100	T	B	mate1 technical by mapping diff	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64267	64267	SRR14428593	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L001 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L001 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L001 R2 001.fastq.gz	SU4_DRT_S2_L001_I1_001.fastq.gz SU4_DRT_S2_L001_R1_001.fastq.gz SU4_DRT_S2_L001_R2_001.fastq.gz	fastq fastq fastq	6902983527.0	54354201.0	GSM5282502 r1	0:8 1:28 2:91	A:1904129671;C:1528133826;G:1597676497;T:1870308784;N:2734749	8	28	91		1904129671	1528133826	1597676497	1870308784	2734749	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93834		0.14712		0.80097		0.53464		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64268	64268	SRR14428594	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L002 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L002 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L002 R2 001.fastq.gz	SU4_DRT_S2_L002_I1_001.fastq.gz SU4_DRT_S2_L002_R1_001.fastq.gz SU4_DRT_S2_L002_R2_001.fastq.gz	fastq fastq fastq	7355984272.0	57921136.0	GSM5282502 r2	0:8 1:28 2:91	A:2029150464;C:1629831151;G:1703134376;T:1991639472;N:2228809	8	28	91		2029150464	1629831151	1703134376	1991639472	2228809	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93751		0.14654		0.80048		0.53568		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64269	64269	SRR14428595	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L003 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L003 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L003 R2 001.fastq.gz	SU4_DRT_S2_L003_I1_001.fastq.gz SU4_DRT_S2_L003_R1_001.fastq.gz SU4_DRT_S2_L003_R2_001.fastq.gz	fastq fastq fastq	6915051321.0	54449223.0	GSM5282502 r3	0:8 1:28 2:91	A:1907859125;C:1531399983;G:1600723047;T:1872767703;N:2301463	8	28	91		1907859125	1531399983	1600723047	1872767703	2301463	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93859		0.14759		0.80075		0.53726		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64270	64270	SRR14428596	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L004 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L004 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L004 R2 001.fastq.gz	SU4_DRT_S2_L004_I1_001.fastq.gz SU4_DRT_S2_L004_R1_001.fastq.gz SU4_DRT_S2_L004_R2_001.fastq.gz	fastq fastq fastq	6496116929.0	51150527.0	GSM5282502 r4	0:8 1:28 2:91	A:1791207713;C:1438082538;G:1503927125;T:1760463486;N:2436067	8	28	91		1791207713	1438082538	1503927125	1760463486	2436067	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93855		0.14517		0.80142		0.51836		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64271	64271	SRR14428597	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L005 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L005 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L005 R2 001.fastq.gz	SU4_DRT_S2_L005_I1_001.fastq.gz SU4_DRT_S2_L005_R1_001.fastq.gz SU4_DRT_S2_L005_R2_001.fastq.gz	fastq fastq fastq	6925225545.0	54529335.0	GSM5282502 r5	0:8 1:28 2:91	A:1908749610;C:1534337999;G:1604298047;T:1874791459;N:3048430	8	28	91		1908749610	1534337999	1604298047	1874791459	3048430	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93705		0.14527		0.79811		0.49961		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64272	64272	SRR14428598	SRX10779735	SRS8866168	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 4	GSM5282502	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282502	GSM5282502: scRNA seq of SU5402 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282502	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282502	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU4 DRT S2 L006 I1 001.fastq.gz read2PairFiles=SU4 DRT S2 L006 R1 001.fastq.gz read3PairFiles=SU4 DRT S2 L006 R2 001.fastq.gz	SU4_DRT_S2_L006_I1_001.fastq.gz SU4_DRT_S2_L006_R1_001.fastq.gz SU4_DRT_S2_L006_R2_001.fastq.gz	fastq fastq fastq	5772764553.0	45454839.0	GSM5282502 r6	0:8 1:28 2:91	A:1592079310;C:1277414314;G:1335013911;T:1565676607;N:2580411	8	28	91		1592079310	1277414314	1335013911	1565676607	2580411	SRX10779735	SRS8866168	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93895		0.1477		0.79772		0.52786		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64273	64273	SRR14428587	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L001 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L001 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L001 R2 001.fastq.gz	SU3_DRT_S1_L001_I1_001.fastq.gz SU3_DRT_S1_L001_R1_001.fastq.gz SU3_DRT_S1_L001_R2_001.fastq.gz	fastq fastq fastq	8251078748.0	64969124.0	GSM5282501 r1	0:8 1:28 2:91	A:2304710369;C:1797342936;G:1900704244;T:2245059790;N:3261409	8	28	91		2304710369	1797342936	1900704244	2245059790	3261409	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92754		0.16532		0.81462		0.52604		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64274	64274	SRR14428588	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L002 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L002 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L002 R2 001.fastq.gz	SU3_DRT_S1_L002_I1_001.fastq.gz SU3_DRT_S1_L002_R1_001.fastq.gz SU3_DRT_S1_L002_R2_001.fastq.gz	fastq fastq fastq	8745931073.0	68865599.0	GSM5282501 r2	0:8 1:28 2:91	A:2444384848;C:1906587775;G:2015145654;T:2377159417;N:2653379	8	28	91		2444384848	1906587775	2015145654	2377159417	2653379	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92881		0.16592		0.8132		0.53153		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64275	64275	SRR14428589	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L003 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L003 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L003 R2 001.fastq.gz	SU3_DRT_S1_L003_I1_001.fastq.gz SU3_DRT_S1_L003_R1_001.fastq.gz SU3_DRT_S1_L003_R2_001.fastq.gz	fastq fastq fastq	8264591040.0	65075520.0	GSM5282501 r3	0:8 1:28 2:91	A:2309308717;C:1801010847;G:1903956632;T:2247562936;N:2751908	8	28	91		2309308717	1801010847	1903956632	2247562936	2751908	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92814		0.16403		0.81186		0.54282		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64276	64276	SRR14428590	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L004 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L004 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L004 R2 001.fastq.gz	SU3_DRT_S1_L004_I1_001.fastq.gz SU3_DRT_S1_L004_R1_001.fastq.gz SU3_DRT_S1_L004_R2_001.fastq.gz	fastq fastq fastq	7798248691.0	61403533.0	GSM5282501 r4	0:8 1:28 2:91	A:2174880077;C:1699441539;G:1797168334;T:2123840121;N:2918620	8	28	91		2174880077	1699441539	1797168334	2123840121	2918620	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92897		0.16544		0.81138		0.53674		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64277	64277	SRR14428591	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L005 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L005 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L005 R2 001.fastq.gz	SU3_DRT_S1_L005_I1_001.fastq.gz SU3_DRT_S1_L005_R1_001.fastq.gz SU3_DRT_S1_L005_R2_001.fastq.gz	fastq fastq fastq	8288550733.0	65264179.0	GSM5282501 r5	0:8 1:28 2:91	A:2310828872;C:1807789428;G:1911417463;T:2254867256;N:3647714	8	28	91		2310828872	1807789428	1911417463	2254867256	3647714	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92759		0.1633		0.81081		0.51359		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64278	64278	SRR14428592	SRX10779734	SRS8866167	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 3	GSM5282501	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282501	GSM5282501: scRNA seq of SU5402 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282501	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282501	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU3 DRT S1 L006 I1 001.fastq.gz read2PairFiles=SU3 DRT S1 L006 R1 001.fastq.gz read3PairFiles=SU3 DRT S1 L006 R2 001.fastq.gz	SU3_DRT_S1_L006_I1_001.fastq.gz SU3_DRT_S1_L006_R1_001.fastq.gz SU3_DRT_S1_L006_R2_001.fastq.gz	fastq fastq fastq	6973058063.0	54905969.0	GSM5282501 r6	0:8 1:28 2:91	A:1944153299;C:1519046931;G:1605222800;T:1901533624;N:3101409	8	28	91		1944153299	1519046931	1605222800	1901533624	3101409	SRX10779734	SRS8866167	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92867		0.16733		0.81063		0.54083		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64279	64279	SRR14428585	SRX10779733	SRS8866166	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 2	GSM5282500	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282500	GSM5282500: scRNA seq of SU5402 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282500	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282500	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU2 DRT S2 L007 I1 001.fastq.gz read2PairFiles=SU2 DRT S2 L007 R1 001.fastq.gz read3PairFiles=SU2 DRT S2 L007 R2 001.fastq.gz	SU2_DRT_S2_L007_I1_001.fastq.gz SU2_DRT_S2_L007_R1_001.fastq.gz SU2_DRT_S2_L007_R2_001.fastq.gz	fastq fastq fastq	22706556822.0	178791786.0	GSM5282500 r1	0:8 1:28 2:91	A:6323509022;C:4887290384;G:5147542675;T:6339376387;N:8838354	8	28	91		6323509022	4887290384	5147542675	6339376387	8838354	SRX10779733	SRS8866166	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92778		0.13822		0.79553		0.51199		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64280	64280	SRR14428586	SRX10779733	SRS8866166	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 2	GSM5282500	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282500	GSM5282500: scRNA seq of SU5402 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282500	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282500	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU2 DRT S2 L008 I1 001.fastq.gz read2PairFiles=SU2 DRT S2 L008 R1 001.fastq.gz read3PairFiles=SU2 DRT S2 L008 R2 001.fastq.gz	SU2_DRT_S2_L008_I1_001.fastq.gz SU2_DRT_S2_L008_R1_001.fastq.gz SU2_DRT_S2_L008_R2_001.fastq.gz	fastq fastq fastq	22610034790.0	178031770.0	GSM5282500 r2	0:8 1:28 2:91	A:6295049786;C:4863549001;G:5125752367;T:6316321559;N:9362077	8	28	91		6295049786	4863549001	5125752367	6316321559	9362077	SRX10779733	SRS8866166	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92707		0.13591		0.79172		0.53017		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64281	64281	SRR14428583	SRX10779732	SRS8866165	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 1	GSM5282499	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282499	GSM5282499: scRNA seq of SU5402 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282499	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282499	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU1 DRT S1 L007 I1 001.fastq.gz read2PairFiles=SU1 DRT S1 L007 R1 001.fastq.gz read3PairFiles=SU1 DRT S1 L007 R2 001.fastq.gz	SU1_DRT_S1_L007_I1_001.fastq.gz SU1_DRT_S1_L007_R1_001.fastq.gz SU1_DRT_S1_L007_R2_001.fastq.gz	fastq fastq fastq	23249060436.0	183063468.0	GSM5282499 r1	0:8 1:28 2:91	A:6473687667;C:5003709390;G:5248540549;T:6514108143;N:9014687	8	28	91		6473687667	5003709390	5248540549	6514108143	9014687	SRX10779732	SRS8866165	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92923		0.129		0.79864		0.55507		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64282	64282	SRR14428584	SRX10779732	SRS8866165	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of SU5402 treatment embryo replicate 1	GSM5282499	tissue:tail\|treatment:SU5402	scRNA seq of SU5402 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:SU5402	GSM5282499	GSM5282499: scRNA seq of SU5402 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282499	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282499	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=SU1 DRT S1 L008 I1 001.fastq.gz read2PairFiles=SU1 DRT S1 L008 R1 001.fastq.gz read3PairFiles=SU1 DRT S1 L008 R2 001.fastq.gz	SU1_DRT_S1_L008_I1_001.fastq.gz SU1_DRT_S1_L008_R1_001.fastq.gz SU1_DRT_S1_L008_R2_001.fastq.gz	fastq fastq fastq	23112024261.0	181984443.0	GSM5282499 r2	0:8 1:28 2:91	A:6437425883;C:4970144751;G:5217204284;T:6477722075;N:9527268	8	28	91		6437425883	4970144751	5217204284	6477722075	9527268	SRX10779732	SRS8866165	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92795		0.12824		0.79707		0.53168		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64283	64283	SRR14428579	SRX10779731	SRS8866164	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 4	GSM5282498	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282498	GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq	GSM5282498	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282498	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG2 DRT S3 L005 I1 001.fastq.gz read2PairFiles=MG2 DRT S3 L005 R1 001.fastq.gz read3PairFiles=MG2 DRT S3 L005 R2 001.fastq.gz	MG2_DRT_S3_L005_I1_001.fastq.gz MG2_DRT_S3_L005_R1_001.fastq.gz MG2_DRT_S3_L005_R2_001.fastq.gz	fastq fastq fastq	9492469966.0	74743858.0	GSM5282498 r1	0:8 1:28 2:91	A:2609486286;C:2069087738;G:2192904289;T:2617283463;N:3708190	8	28	91		2609486286	2069087738	2192904289	2617283463	3708190	SRX10779731	SRS8866164	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92805		0.11402		0.80227		0.48223		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64284	64284	SRR14428580	SRX10779731	SRS8866164	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 4	GSM5282498	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282498	GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq	GSM5282498	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282498	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG2 DRT S3 L006 I1 001.fastq.gz read2PairFiles=MG2 DRT S3 L006 R1 001.fastq.gz read3PairFiles=MG2 DRT S3 L006 R2 001.fastq.gz	MG2_DRT_S3_L006_I1_001.fastq.gz MG2_DRT_S3_L006_R1_001.fastq.gz MG2_DRT_S3_L006_R2_001.fastq.gz	fastq fastq fastq	9635960027.0	75873701.0	GSM5282498 r2	0:8 1:28 2:91	A:2647293422;C:2103232371;G:2225407295;T:2656262617;N:3764322	8	28	91		2647293422	2103232371	2225407295	2656262617	3764322	SRX10779731	SRS8866164	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92692		0.11501		0.80403		0.48189		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64285	64285	SRR14428581	SRX10779731	SRS8866164	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 4	GSM5282498	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282498	GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq	GSM5282498	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282498	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG2 DRT S3 L007 I1 001.fastq.gz read2PairFiles=MG2 DRT S3 L007 R1 001.fastq.gz read3PairFiles=MG2 DRT S3 L007 R2 001.fastq.gz	MG2_DRT_S3_L007_I1_001.fastq.gz MG2_DRT_S3_L007_R1_001.fastq.gz MG2_DRT_S3_L007_R2_001.fastq.gz	fastq fastq fastq	9387531390.0	73917570.0	GSM5282498 r3	0:8 1:28 2:91	A:2579905219;C:2047020899;G:2168062814;T:2588424779;N:4117679	8	28	91		2579905219	2047020899	2168062814	2588424779	4117679	SRX10779731	SRS8866164	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92666		0.11505		0.80529		0.49382		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64286	64286	SRR14428582	SRX10779731	SRS8866164	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 4	GSM5282498	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282498	GSM5282498: scRNA seq of Wild type embryo replicate 4; Danio rerio; RNA Seq	GSM5282498	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282498	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG2 DRT S3 L008 I1 001.fastq.gz read2PairFiles=MG2 DRT S3 L008 R1 001.fastq.gz read3PairFiles=MG2 DRT S3 L008 R2 001.fastq.gz	MG2_DRT_S3_L008_I1_001.fastq.gz MG2_DRT_S3_L008_R1_001.fastq.gz MG2_DRT_S3_L008_R2_001.fastq.gz	fastq fastq fastq	9217689464.0	72580232.0	GSM5282498 r4	0:8 1:28 2:91	A:2533345035;C:2008536731;G:2129886197;T:2541165144;N:4756357	8	28	91		2533345035	2008536731	2129886197	2541165144	4756357	SRX10779731	SRS8866164	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92286		0.11529		0.80395		0.48636		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64287	64287	SRR14428575	SRX10779730	SRS8866163	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 3	GSM5282497	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282497	GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq	GSM5282497	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282497	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG1 DRT S2 L005 I1 001.fastq.gz read2PairFiles=MG1 DRT S2 L005 R1 001.fastq.gz read3PairFiles=MG1 DRT S2 L005 R2 001.fastq.gz	MG1_DRT_S2_L005_I1_001.fastq.gz MG1_DRT_S2_L005_R1_001.fastq.gz MG1_DRT_S2_L005_R2_001.fastq.gz	fastq fastq fastq	17349575664.0	136610832.0	GSM5282497 r1	0:8 1:28 2:91	A:4818340596;C:3752070379;G:3990473269;T:4781914390;N:6777030	8	28	91		4818340596	3752070379	3990473269	4781914390	6777030	SRX10779730	SRS8866163	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.9284		0.10948		0.80547		0.49189		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64288	64288	SRR14428576	SRX10779730	SRS8866163	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 3	GSM5282497	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282497	GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq	GSM5282497	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282497	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG1 DRT S2 L006 I1 001.fastq.gz read2PairFiles=MG1 DRT S2 L006 R1 001.fastq.gz read3PairFiles=MG1 DRT S2 L006 R2 001.fastq.gz	MG1_DRT_S2_L006_I1_001.fastq.gz MG1_DRT_S2_L006_R1_001.fastq.gz MG1_DRT_S2_L006_R2_001.fastq.gz	fastq fastq fastq	17618903294.0	138731522.0	GSM5282497 r2	0:8 1:28 2:91	A:4890473222;C:3815291120;G:4050726863;T:4855538370;N:6873719	8	28	91		4890473222	3815291120	4050726863	4855538370	6873719	SRX10779730	SRS8866163	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92706		0.1099		0.80543		0.49186		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64289	64289	SRR14428577	SRX10779730	SRS8866163	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 3	GSM5282497	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282497	GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq	GSM5282497	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282497	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG1 DRT S2 L007 I1 001.fastq.gz read2PairFiles=MG1 DRT S2 L007 R1 001.fastq.gz read3PairFiles=MG1 DRT S2 L007 R2 001.fastq.gz	MG1_DRT_S2_L007_I1_001.fastq.gz MG1_DRT_S2_L007_R1_001.fastq.gz MG1_DRT_S2_L007_R2_001.fastq.gz	fastq fastq fastq	17163315178.0	135144214.0	GSM5282497 r3	0:8 1:28 2:91	A:4766251435;C:3713084450;G:3945754157;T:4730698036;N:7527100	8	28	91		4766251435	3713084450	3945754157	4730698036	7527100	SRX10779730	SRS8866163	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92754		0.10835		0.80797		0.48866		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64290	64290	SRR14428578	SRX10779730	SRS8866163	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 3	GSM5282497	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282497	GSM5282497: scRNA seq of Wild type embryo replicate 3; Danio rerio; RNA Seq	GSM5282497	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282497	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=MG1 DRT S2 L008 I1 001.fastq.gz read2PairFiles=MG1 DRT S2 L008 R1 001.fastq.gz read3PairFiles=MG1 DRT S2 L008 R2 001.fastq.gz	MG1_DRT_S2_L008_I1_001.fastq.gz MG1_DRT_S2_L008_R1_001.fastq.gz MG1_DRT_S2_L008_R2_001.fastq.gz	fastq fastq fastq	16809702347.0	132359861.0	GSM5282497 r4	0:8 1:28 2:91	A:4667371642;C:3633855882;G:3867101355;T:4632748337;N:8625131	8	28	91		4667371642	3633855882	3867101355	4632748337	8625131	SRX10779730	SRS8866163	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92328		0.10721		0.80367		0.47808		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64291	64291	SRR14428569	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L001 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L001 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L001 R2 001.fastq.gz	DMH4_DRT_S6_L001_I1_001.fastq.gz DMH4_DRT_S6_L001_R1_001.fastq.gz DMH4_DRT_S6_L001_R2_001.fastq.gz	fastq fastq fastq	7123207877.0	56088251.0	GSM5282496 r1	0:8 1:28 2:91	A:1962729920;C:1588676173;G:1649353500;T:1919637412;N:2810872	8	28	91		1962729920	1588676173	1649353500	1919637412	2810872	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93588		0.14896		0.79758		0.49446		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64292	64292	SRR14428570	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L002 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L002 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L002 R2 001.fastq.gz	DMH4_DRT_S6_L002_I1_001.fastq.gz DMH4_DRT_S6_L002_R1_001.fastq.gz DMH4_DRT_S6_L002_R2_001.fastq.gz	fastq fastq fastq	7586038422.0	59732586.0	GSM5282496 r2	0:8 1:28 2:91	A:2091122151;C:1693169697;G:1756654249;T:2042799697;N:2292628	8	28	91		2091122151	1693169697	1756654249	2042799697	2292628	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93788		0.15089		0.79634		0.5178		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64293	64293	SRR14428571	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L003 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L003 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L003 R2 001.fastq.gz	DMH4_DRT_S6_L003_I1_001.fastq.gz DMH4_DRT_S6_L003_R1_001.fastq.gz DMH4_DRT_S6_L003_R2_001.fastq.gz	fastq fastq fastq	7142674183.0	56241529.0	GSM5282496 r3	0:8 1:28 2:91	A:1968941716;C:1593511481;G:1653686658;T:1924167092;N:2367236	8	28	91		1968941716	1593511481	1653686658	1924167092	2367236	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93752		0.14955		0.79644		0.50838		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64294	64294	SRR14428572	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L004 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L004 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L004 R2 001.fastq.gz	DMH4_DRT_S6_L004_I1_001.fastq.gz DMH4_DRT_S6_L004_R1_001.fastq.gz DMH4_DRT_S6_L004_R2_001.fastq.gz	fastq fastq fastq	6713707045.0	52863835.0	GSM5282496 r4	0:8 1:28 2:91	A:1848906888;C:1497203954;G:1554812611;T:1810277268;N:2506324	8	28	91		1848906888	1497203954	1554812611	1810277268	2506324	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93754		0.1505		0.79553		0.52685		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64295	64295	SRR14428573	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L005 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L005 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L005 R2 001.fastq.gz	DMH4_DRT_S6_L005_I1_001.fastq.gz DMH4_DRT_S6_L005_R1_001.fastq.gz DMH4_DRT_S6_L005_R2_001.fastq.gz	fastq fastq fastq	7157753782.0	56360266.0	GSM5282496 r5	0:8 1:28 2:91	A:1970673839;C:1597733780;G:1658449707;T:1927756569;N:3139887	8	28	91		1970673839	1597733780	1658449707	1927756569	3139887	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93636		0.14837		0.79545		0.52489		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64296	64296	SRR14428574	SRX10779729	SRS8866162	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 4	GSM5282496	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 4	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282496	GSM5282496: scRNA seq of DMH1 treatment embryo replicate 4; Danio rerio; RNA Seq	GSM5282496	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282496	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH4 DRT S6 L006 I1 001.fastq.gz read2PairFiles=DMH4 DRT S6 L006 R1 001.fastq.gz read3PairFiles=DMH4 DRT S6 L006 R2 001.fastq.gz	DMH4_DRT_S6_L006_I1_001.fastq.gz DMH4_DRT_S6_L006_R1_001.fastq.gz DMH4_DRT_S6_L006_R2_001.fastq.gz	fastq fastq fastq	5969524129.0	47004127.0	GSM5282496 r6	0:8 1:28 2:91	A:1643952599;C:1330790681;G:1381135714;T:1610997620;N:2647515	8	28	91		1643952599	1330790681	1381135714	1610997620	2647515	SRX10779729	SRS8866162	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93633		0.15123		0.7959		0.5171		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64297	64297	SRR14428563	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L001 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L001 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L001 R2 001.fastq.gz	DMH3_DRT_S5_L001_I1_001.fastq.gz DMH3_DRT_S5_L001_R1_001.fastq.gz DMH3_DRT_S5_L001_R2_001.fastq.gz	fastq fastq fastq	7192416908.0	56633204.0	GSM5282495 r1	0:8 1:28 2:91	A:1991209107;C:1581442528;G:1671432113;T:1945488801;N:2844359	8	28	91		1991209107	1581442528	1671432113	1945488801	2844359	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93559		0.16137		0.80133		0.52562		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64298	64298	SRR14428564	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L002 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L002 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L002 R2 001.fastq.gz	DMH3_DRT_S5_L002_I1_001.fastq.gz DMH3_DRT_S5_L002_R1_001.fastq.gz DMH3_DRT_S5_L002_R2_001.fastq.gz	fastq fastq fastq	7657698553.0	60296839.0	GSM5282495 r2	0:8 1:28 2:91	A:2120078045;C:1685386017;G:1780204812;T:2069712107;N:2317572	8	28	91		2120078045	1685386017	1780204812	2069712107	2317572	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93524		0.16046		0.80282		0.53593		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64299	64299	SRR14428565	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L003 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L003 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L003 R2 001.fastq.gz	DMH3_DRT_S5_L003_I1_001.fastq.gz DMH3_DRT_S5_L003_R1_001.fastq.gz DMH3_DRT_S5_L003_R2_001.fastq.gz	fastq fastq fastq	7209380044.0	56766772.0	GSM5282495 r3	0:8 1:28 2:91	A:1996356430;C:1585660923;G:1675622569;T:1949346223;N:2393899	8	28	91		1996356430	1585660923	1675622569	1949346223	2393899	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93589		0.16061		0.79896		0.53735		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64300	64300	SRR14428566	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L004 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L004 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L004 R2 001.fastq.gz	DMH3_DRT_S5_L004_I1_001.fastq.gz DMH3_DRT_S5_L004_R1_001.fastq.gz DMH3_DRT_S5_L004_R2_001.fastq.gz	fastq fastq fastq	6776552233.0	53358679.0	GSM5282495 r4	0:8 1:28 2:91	A:1875578465;C:1489508714;G:1575289055;T:1833640279;N:2535720	8	28	91		1875578465	1489508714	1575289055	1833640279	2535720	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93499		0.16117		0.79862		0.55002		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64301	64301	SRR14428567	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L005 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L005 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L005 R2 001.fastq.gz	DMH3_DRT_S5_L005_R2_001.fastq.gz DMH3_DRT_S5_L005_R1_001.fastq.gz DMH3_DRT_S5_L005_I1_001.fastq.gz	fastq fastq fastq	7225366042.0	56892646.0	GSM5282495 r5	0:8 1:28 2:91	A:1998880759;C:1589714962;G:1680768850;T:1952828313;N:3173158	8	28	91		1998880759	1589714962	1680768850	1952828313	3173158	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93582		0.16069		0.79876		0.52951		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64302	64302	SRR14428568	SRX10779728	SRS8866161	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 3	GSM5282495	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 3	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282495	GSM5282495: scRNA seq of DMH1 treatment embryo replicate 3; Danio rerio; RNA Seq	GSM5282495	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282495	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH3 DRT S5 L006 I1 001.fastq.gz read2PairFiles=DMH3 DRT S5 L006 R1 001.fastq.gz read3PairFiles=DMH3 DRT S5 L006 R2 001.fastq.gz	DMH3_DRT_S5_L006_I1_001.fastq.gz DMH3_DRT_S5_L006_R1_001.fastq.gz DMH3_DRT_S5_L006_R2_001.fastq.gz	fastq fastq fastq	6030562234.0	47484742.0	GSM5282495 r6	0:8 1:28 2:91	A:1669516878;C:1324814074;G:1400296411;T:1633256111;N:2678760	8	28	91		1669516878	1324814074	1400296411	1633256111	2678760	SRX10779728	SRS8866161	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93567		0.16207		0.79821		0.54157		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64303	64303	SRR14428557	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L001 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L001 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L001 R2 001.fastq.gz	DMH2_DRT_S4_L001_I1_001.fastq.gz DMH2_DRT_S4_L001_R1_001.fastq.gz DMH2_DRT_S4_L001_R2_001.fastq.gz	fastq fastq fastq	6255378523.0	49254949.0	GSM5282494 r1	0:8 1:28 2:91	A:1738029934;C:1358217459;G:1451180213;T:1705471817;N:2479100	8	28	91		1738029934	1358217459	1451180213	1705471817	2479100	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93582		0.15096		0.80066		0.51934		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64304	64304	SRR14428558	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L002 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L002 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L002 R2 001.fastq.gz	DMH2_DRT_S4_L002_I1_001.fastq.gz DMH2_DRT_S4_L002_R1_001.fastq.gz DMH2_DRT_S4_L002_R2_001.fastq.gz	fastq fastq fastq	6646362882.0	52333566.0	GSM5282494 r2	0:8 1:28 2:91	A:1846304900;C:1444524063;G:1542630967;T:1810887938;N:2015014	8	28	91		1846304900	1444524063	1542630967	1810887938	2015014	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93778		0.14911		0.80014		0.53536		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64305	64305	SRR14428559	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L003 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L003 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L003 R2 001.fastq.gz	DMH2_DRT_S4_L003_I1_001.fastq.gz DMH2_DRT_S4_L003_R1_001.fastq.gz DMH2_DRT_S4_L003_R2_001.fastq.gz	fastq fastq fastq	6270391447.0	49373161.0	GSM5282494 r3	0:8 1:28 2:91	A:1742421104;C:1361864013;G:1454871057;T:1709147257;N:2088016	8	28	91		1742421104	1361864013	1454871057	1709147257	2088016	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93712		0.14875		0.79941		0.53579		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64306	64306	SRR14428560	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L004 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L004 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L004 R2 001.fastq.gz	DMH2_DRT_S4_L004_I1_001.fastq.gz DMH2_DRT_S4_L004_R1_001.fastq.gz DMH2_DRT_S4_L004_R2_001.fastq.gz	fastq fastq fastq	5907875535.0	46518705.0	GSM5282494 r4	0:8 1:28 2:91	A:1640954912;C:1282401213;G:1370906184;T:1611398475;N:2214751	8	28	91		1640954912	1282401213	1370906184	1611398475	2214751	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93572		0.15069		0.79955		0.5303		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64307	64307	SRR14428561	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L005 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L005 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L005 R2 001.fastq.gz	DMH2_DRT_S4_L005_I1_001.fastq.gz DMH2_DRT_S4_L005_R1_001.fastq.gz DMH2_DRT_S4_L005_R2_001.fastq.gz	fastq fastq fastq	6282717178.0	49470214.0	GSM5282494 r5	0:8 1:28 2:91	A:1743975533;C:1365224270;G:1459015324;T:1711737289;N:2764762	8	28	91		1743975533	1365224270	1459015324	1711737289	2764762	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93674		0.14955		0.79967		0.53737		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64308	64308	SRR14428562	SRX10779727	SRS8866160	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 2	GSM5282494	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282494	GSM5282494: scRNA seq of DMH1 treatment embryo replicate 2; Danio rerio; RNA Seq	GSM5282494	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282494	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH2 DRT S4 L006 I1 001.fastq.gz read2PairFiles=DMH2 DRT S4 L006 R1 001.fastq.gz read3PairFiles=DMH2 DRT S4 L006 R2 001.fastq.gz	DMH2_DRT_S4_L006_I1_001.fastq.gz DMH2_DRT_S4_L006_R1_001.fastq.gz DMH2_DRT_S4_L006_R2_001.fastq.gz	fastq fastq fastq	5269518417.0	41492271.0	GSM5282494 r6	0:8 1:28 2:91	A:1464198453;C:1143221188;G:1221184805;T:1438563475;N:2350496	8	28	91		1464198453	1143221188	1221184805	1438563475	2350496	SRX10779727	SRS8866160	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93742		0.14919		0.79845		0.54799		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64309	64309	SRR14428551	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L001 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L001 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L001 R2 001.fastq.gz	DMH0_DRT_S3_L001_I1_001.fastq.gz DMH0_DRT_S3_L001_R1_001.fastq.gz DMH0_DRT_S3_L001_R2_001.fastq.gz	fastq fastq fastq	6300938503.0	49613689.0	GSM5282493 r1	0:8 1:28 2:91	A:1759925650;C:1368738360;G:1447709330;T:1722055328;N:2509835	8	28	91		1759925650	1368738360	1447709330	1722055328	2509835	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.9327		0.15731		0.80342		0.52216		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64310	64310	SRR14428552	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L002 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L002 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L002 R2 001.fastq.gz	DMH0_DRT_S3_L002_I1_001.fastq.gz DMH0_DRT_S3_L002_R1_001.fastq.gz DMH0_DRT_S3_L002_R2_001.fastq.gz	fastq fastq fastq	6688754085.0	52667355.0	GSM5282493 r2	0:8 1:28 2:91	A:1871898974;C:1453608653;G:1536025145;T:1825187880;N:2033433	8	28	91		1871898974	1453608653	1536025145	1825187880	2033433	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93334		0.1552		0.80373		0.50289		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64311	64311	SRR14428553	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L003 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L003 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L003 R2 001.fastq.gz	DMH0_DRT_S3_L003_I1_001.fastq.gz DMH0_DRT_S3_L003_R1_001.fastq.gz DMH0_DRT_S3_L003_R2_001.fastq.gz	fastq fastq fastq	6309453345.0	49680735.0	GSM5282493 r3	0:8 1:28 2:91	A:1763855982;C:1371096919;G:1449223687;T:1723174913;N:2101844	8	28	91		1763855982	1371096919	1449223687	1723174913	2101844	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93296		0.15857		0.80129		0.51279		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64312	64312	SRR14428554	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L004 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L004 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L004 R2 001.fastq.gz	DMH0_DRT_S3_L004_I1_001.fastq.gz DMH0_DRT_S3_L004_R1_001.fastq.gz DMH0_DRT_S3_L004_R2_001.fastq.gz	fastq fastq fastq	5945234490.0	46812870.0	GSM5282493 r4	0:8 1:28 2:91	A:1658145096;C:1291985068;G:1366762922;T:1626114511;N:2226893	8	28	91		1658145096	1291985068	1366762922	1626114511	2226893	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93141		0.15528		0.80046		0.51469		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64313	64313	SRR14428555	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L005 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L005 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L005 R2 001.fastq.gz	DMH0_DRT_S3_L005_I1_001.fastq.gz DMH0_DRT_S3_L005_R1_001.fastq.gz DMH0_DRT_S3_L005_R2_001.fastq.gz	fastq fastq fastq	6320557082.0	49768166.0	GSM5282493 r5	0:8 1:28 2:91	A:1763393223;C:1374562319;G:1453442879;T:1726374884;N:2783777	8	28	91		1763393223	1374562319	1453442879	1726374884	2783777	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93108		0.15583		0.79797		0.49781		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64314	64314	SRR14428556	SRX10779726	SRS8866159	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of DMH1 treatment embryo replicate 1	GSM5282493	tissue:tail\|treatment:DMH1	scRNA seq of DMH1 treatment embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:DMH1	GSM5282493	GSM5282493: scRNA seq of DMH1 treatment embryo replicate 1; Danio rerio; RNA Seq	GSM5282493	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282493	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DMH0 DRT S3 L006 I1 001.fastq.gz read2PairFiles=DMH0 DRT S3 L006 R1 001.fastq.gz read3PairFiles=DMH0 DRT S3 L006 R2 001.fastq.gz	DMH0_DRT_S3_L006_I1_001.fastq.gz DMH0_DRT_S3_L006_R1_001.fastq.gz DMH0_DRT_S3_L006_R2_001.fastq.gz	fastq fastq fastq	5301340553.0	41742839.0	GSM5282493 r6	0:8 1:28 2:91	A:1476841423;C:1152107488;G:1217817934;T:1452213447;N:2360261	8	28	91		1476841423	1152107488	1217817934	1452213447	2360261	SRX10779726	SRS8866159	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.93212		0.15734		0.79762		0.5013		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64315	64315	SRR14428547	SRX10779725	SRS8866158	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 2	GSM5282492	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282492	GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq	GSM5282492	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282492	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ2 DRT S5 L005 I1 001.fastq.gz read2PairFiles=DJ2 DRT S5 L005 R1 001.fastq.gz read3PairFiles=DJ2 DRT S5 L005 R2 001.fastq.gz	DJ2_DRT_S5_L005_I1_001.fastq.gz DJ2_DRT_S5_L005_R1_001.fastq.gz DJ2_DRT_S5_L005_R2_001.fastq.gz	fastq fastq fastq	9467670930.0	74548590.0	GSM5282492 r1	0:8 1:28 2:91	A:2616039420;C:2044228336;G:2155133373;T:2648580130;N:3689671	8	28	91		2616039420	2044228336	2155133373	2648580130	3689671	SRX10779725	SRS8866158	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92297		0.1292		0.79594		0.47206		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64316	64316	SRR14428548	SRX10779725	SRS8866158	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 2	GSM5282492	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282492	GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq	GSM5282492	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282492	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ2 DRT S5 L006 I1 001.fastq.gz read2PairFiles=DJ2 DRT S5 L006 R1 001.fastq.gz read3PairFiles=DJ2 DRT S5 L006 R2 001.fastq.gz	DJ2_DRT_S5_L006_I1_001.fastq.gz DJ2_DRT_S5_L006_R1_001.fastq.gz DJ2_DRT_S5_L006_R2_001.fastq.gz	fastq fastq fastq	9606615153.0	75642639.0	GSM5282492 r2	0:8 1:28 2:91	A:2652932569;C:2076799397;G:2185712596;T:2687420468;N:3750123	8	28	91		2652932569	2076799397	2185712596	2687420468	3750123	SRX10779725	SRS8866158	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92257		0.12971		0.79659		0.48836		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64317	64317	SRR14428549	SRX10779725	SRS8866158	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 2	GSM5282492	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282492	GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq	GSM5282492	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282492	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ2 DRT S5 L007 I1 001.fastq.gz read2PairFiles=DJ2 DRT S5 L007 R1 001.fastq.gz read3PairFiles=DJ2 DRT S5 L007 R2 001.fastq.gz	DJ2_DRT_S5_L007_I1_001.fastq.gz DJ2_DRT_S5_L007_R1_001.fastq.gz DJ2_DRT_S5_L007_R2_001.fastq.gz	fastq fastq fastq	9361056081.0	73709103.0	GSM5282492 r3	0:8 1:28 2:91	A:2586073553;C:2021754649;G:2129759929;T:2619378296;N:4089654	8	28	91		2586073553	2021754649	2129759929	2619378296	4089654	SRX10779725	SRS8866158	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.92292		0.12805		0.79711		0.48448		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64318	64318	SRR14428550	SRX10779725	SRS8866158	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 2	GSM5282492	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 2	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282492	GSM5282492: scRNA seq of Wild type embryo replicate 2; Danio rerio; RNA Seq	GSM5282492	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282492	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ2 DRT S5 L008 I1 001.fastq.gz read2PairFiles=DJ2 DRT S5 L008 R1 001.fastq.gz read3PairFiles=DJ2 DRT S5 L008 R2 001.fastq.gz	DJ2_DRT_S5_L008_I1_001.fastq.gz DJ2_DRT_S5_L008_R1_001.fastq.gz DJ2_DRT_S5_L008_R2_001.fastq.gz	fastq fastq fastq	9160620617.0	72130871.0	GSM5282492 r4	0:8 1:28 2:91	A:2531032919;C:1977019121;G:2085046454;T:2562829034;N:4693089	8	28	91		2531032919	1977019121	2085046454	2562829034	4693089	SRX10779725	SRS8866158	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.91651		0.12813		0.79525		0.48008		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64319	64319	SRR14428543	SRX10779724	SRS8866157	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 1	GSM5282491	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282491	GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq	GSM5282491	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ1 DRT S4 L005 I1 001.fastq.gz read2PairFiles=DJ1 DRT S4 L005 R1 001.fastq.gz read3PairFiles=DJ1 DRT S4 L005 R2 001.fastq.gz	DJ1_DRT_S4_L005_I1_001.fastq.gz DJ1_DRT_S4_L005_R1_001.fastq.gz DJ1_DRT_S4_L005_R2_001.fastq.gz	fastq fastq fastq	9659035419.0	76055397.0	GSM5282491 r1	0:8 1:28 2:91	A:2699725431;C:2071581042;G:2198625287;T:2685342644;N:3761015	8	28	91		2699725431	2071581042	2198625287	2685342644	3761015	SRX10779724	SRS8866157	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.91607		0.12753		0.79681		0.49967		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64320	64320	SRR14428544	SRX10779724	SRS8866157	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 1	GSM5282491	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282491	GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq	GSM5282491	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ1 DRT S4 L006 I1 001.fastq.gz read2PairFiles=DJ1 DRT S4 L006 R1 001.fastq.gz read3PairFiles=DJ1 DRT S4 L006 R2 001.fastq.gz	DJ1_DRT_S4_L006_I1_001.fastq.gz DJ1_DRT_S4_L006_R1_001.fastq.gz DJ1_DRT_S4_L006_R2_001.fastq.gz	fastq fastq fastq	9813486723.0	77271549.0	GSM5282491 r2	0:8 1:28 2:91	A:2741133797;C:2108031651;G:2232840506;T:2727650204;N:3830565	8	28	91		2741133797	2108031651	2232840506	2727650204	3830565	SRX10779724	SRS8866157	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.91637		0.12716		0.8002		0.49381		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64321	64321	SRR14428545	SRX10779724	SRS8866157	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 1	GSM5282491	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282491	GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq	GSM5282491	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ1 DRT S4 L007 I1 001.fastq.gz read2PairFiles=DJ1 DRT S4 L007 R1 001.fastq.gz read3PairFiles=DJ1 DRT S4 L007 R2 001.fastq.gz	DJ1_DRT_S4_L007_I1_001.fastq.gz DJ1_DRT_S4_L007_R1_001.fastq.gz DJ1_DRT_S4_L007_R2_001.fastq.gz	fastq fastq fastq	9552161363.0	75213869.0	GSM5282491 r3	0:8 1:28 2:91	A:2669841244;C:2049417390;G:2172764722;T:2655952220;N:4185787	8	28	91		2669841244	2049417390	2172764722	2655952220	4185787	SRX10779724	SRS8866157	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.9169		0.1274		0.79975		0.48564		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-system
64322	64322	SRR14428546	SRX10779724	SRS8866157	SRP318543	PRJNA727493	Single cell gene expression analysis of zebrafish body elongation	GSE173894	Transcriptome Analysis	scRNA seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt Fgf and BMP signaling pathway. Overall design: We performed single cell RNA sequencing scRNAseq on dissected tails from 10 12 somite stage zebrafish embryos. We used wild type embryos and embryos subject to treatments known to alter tailbud cell migration specifically inhibition of FGF BMP or Wnt signaling. For each treatment we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30 000 35 000 single cell profiles.	pubmed:37267354	scRNA seq of Wild type embryo replicate 1	GSM5282491	tissue:tail\|treatment:WT	scRNA seq of Wild type embryo replicate 1	We aligned the scRNA seq data to Grcz11 and demultiplexed using Cell Ranger 10X Genomics version 3.0. Genome build: Grcz11 Supplementary files format and content: Matrix market file for UMI counts. TSV file for annotation such as clustering results. TXT files for cell barcodes column labels for MTX file and gene names row labels for MTX file.	tail	Embryos were incubated until the 10 12 somite stage and then dissected in ice cold Hank’s Balanced Salt Solution. The tail was collected by cutting immediately posterior to the last formed somite. Groups of tails consisting of ten tails for wild type FGF or BMP inhibition or twelve tails for Wnt inhibition were pooled together.	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell 3’ Library produces a standard…		treatment:WT	GSM5282491	GSM5282491: scRNA seq of Wild type embryo replicate 1; Danio rerio; RNA Seq	GSM5282491	1	Cells were dissociated by incubation in 20 U/mL papain solution Worthing Biochemical for 15 minutes at 29 °C with gentle agitation. Halfway through the incubation the solution was triturated ten times with a P200 pipette. Cells were spun down at 300g for five minutes and then resuspended in 40 L of cold HBSS. Cell concentration and viability were checked with a hemocytometer and the volume of the solution was adjusted if required. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partition with a pool of about 750 000 barcoded gel beads to form nanoliter scale Gel Beads In Emulsions GEMs. Each gel bead has primers containing i an Illumina R1 sequence read 1 sequencing primer ii a 16 nt 10x Barcode iii a 10 nt Unique Molecular Identifier UMI and iv a poly dT primer sequence. Upon dissolution of the Gel Beads in a GEM the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded full length cDNA from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size prior to library construction. R1 read 1 primer sequence were added to the molecules during GEM incubation. P5 P7 a sample index and R2 read 2 primer sequence were added during library construction via End Repair A tailing Adaptor Ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. The Single Cell three prime Protocol produces Illumina ready sequencing libraries. A Single Cell three prime Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell three prime 16 bp 10x Barcode and 10 bp UMI are encoded in Read 1 while Read 2 is used to sequence the cDNA fragment. Sequencing a Single Cell thr…	GEO Accession:GSM5282491	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP318543	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=DJ1 DRT S4 L008 I1 001.fastq.gz read2PairFiles=DJ1 DRT S4 L008 R1 001.fastq.gz read3PairFiles=DJ1 DRT S4 L008 R2 001.fastq.gz	DJ1_DRT_S4_L008_I1_001.fastq.gz DJ1_DRT_S4_L008_R1_001.fastq.gz DJ1_DRT_S4_L008_R2_001.fastq.gz	fastq fastq fastq	9341088506.0	73551878.0	GSM5282491 r4	0:8 1:28 2:91	A:2610958437;C:2002300297;G:2125775231;T:2597251940;N:4802601	8	28	91		2610958437	2002300297	2125775231	2597251940	4802601	SRX10779724	SRS8866157	SRA1228423	GEO	Yale Science Building, Room 106, Department of Molecular, Cellular and Developmental Biology, Yale University	1	0.91008		0.12627		0.79973		0.49782		91		B		usable mapping rate	illumina	hiseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x	United States	2021-05-05	Segmentation	Embryo	Tail	Multi-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");;