metadata: run_metadata: 171 rows where experiment.library_selection = "cDNA", experiment.library_strategy = "RNA-Seq" and technology = "scartrace"

171 rows where experiment.library_selection = "cDNA", experiment.library_strategy = "RNA-Seq" and technology = "scartrace"

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.extractprotocol	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.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.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
43465	43465	SRR6888838	SRX3839388	SRS3086676	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 WKM Scar	GSM3065994	tissue:WKM single cells\|cas9 injection:protein\|FISH id:P2\|organ:WKM\|sorted plates:2	P2 WKM Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	WKM single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:WKM\|sorted plates:2	GSM3065994	GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq	GSM3065994	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065994	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-WKM-001-Scar_R1.fastq.gz P2-WKM-001-Scar_R2.fastq.gz	fastq fastq	344288293.0	2265619.0	GSM3065994 r1	0:75.98 1:75.98	A:60840077;C:100295730;G:126071444;T:57044397;N:36645	75	75	60840077	100295730	126071444	57044397	36645	SRX3839388	SRS3086676	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0007	0.00458	0.00047	0.00268	0.99971	0.99669	0.37837	0.42452	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Undetermined	Undetermined
43466	43466	SRR6888839	SRX3839388	SRS3086676	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 WKM Scar	GSM3065994	tissue:WKM single cells\|cas9 injection:protein\|FISH id:P2\|organ:WKM\|sorted plates:2	P2 WKM Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	WKM single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:WKM\|sorted plates:2	GSM3065994	GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq	GSM3065994	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065994	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-WKM-002-Scar_R1.fastq.gz P2-WKM-002-Scar_R2.fastq.gz	fastq fastq	717066879.0	4719933.0	GSM3065994 r2	0:75.98 1:75.94	A:126563252;C:209265530;G:262732780;T:118432095;N:73222	75	75	126563252	209265530	262732780	118432095	73222	SRX3839388	SRS3086676	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00063	0.1196	0.00034	0.0666	0.99977	0.99598	0.23529	0.45161	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Undetermined	Undetermined
43467	43467	SRR6888837	SRX3839387	SRS3086675	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 right midbrain Scar	GSM3065993	tissue:right midbrain single cells\|cas9 injection:protein\|FISH id:P2\|organ:right midbrain\|sorted plates:1	P2 right midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:right midbrain\|sorted plates:1	GSM3065993	GSM3065993: P2 right midbrain Scar; Danio rerio; RNA Seq	GSM3065993	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065993	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-Midbrain-right-p01-Scar_R1.fastq.gz P2-Midbrain-right-p01-Scar_R2.fastq.gz	fastq fastq	152826307.0	1005857.0	GSM3065993 r1	0:75.98 1:75.95	A:27775284;C:45270196;G:56312550;T:23417130;N:51147	75	75	27775284	45270196	56312550	23417130	51147	SRX3839387	SRS3086675	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00023	0.00037	0.0002	0.00032	0.99993	0.99985	0.0	0.42857	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Brain	Nervous System
43468	43468	SRR6888836	SRX3839386	SRS3086673	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 left midbrain Scar	GSM3065992	tissue:left midbrain single cells\|cas9 injection:protein\|FISH id:P2\|organ:left midbrain\|sorted plates:1	P2 left midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:left midbrain\|sorted plates:1	GSM3065992	GSM3065992: P2 left midbrain Scar; Danio rerio; RNA Seq	GSM3065992	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065992	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-Midbrain-left-p01-Scar_R2.fastq.gz P2-Midbrain-left-p01-Scar_R1.fastq.gz	fastq fastq	98906805.0	650967.0	GSM3065992 r1	0:75.98 1:75.96	A:17838466;C:29265024;G:36491674;T:15282661;N:28980	75	75	17838466	29265024	36491674	15282661	28980	SRX3839386	SRS3086673	SRA602108	GEO	AVO, Hubrecht Institue	2	1e-05	1e-05	0.0	0.0	0.99997	0.99997	0.0	0.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Brain	Nervous System
43469	43469	SRR6888835	SRX3839385	SRS3086671	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 forebrain Scar	GSM3065991	tissue:forebrain single cells\|cas9 injection:protein\|FISH id:P2\|organ:forebrain\|sorted plates:1	P2 forebrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	forebrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:forebrain\|sorted plates:1	GSM3065991	GSM3065991: P2 forebrain Scar; Danio rerio; RNA Seq	GSM3065991	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065991	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-Forebrain-p01-Scar_R2.fastq.gz P2-Forebrain-p01-Scar_R1.fastq.gz	fastq fastq	39304298.0	259048.0	GSM3065991 r1	0:75.93 1:75.80	A:7719394;C:11234773;G:13950579;T:6398707;N:845	75	75	7719394	11234773	13950579	6398707	845	SRX3839385	SRS3086671	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00783	0.00436	0.00683	0.00405	0.99989	0.99945	0.01265	0.48148	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Brain	Nervous System
43470	43470	SRR6888834	SRX3839384	SRS3086672	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 right eye Scar	GSM3065990	tissue:right eye single cells\|cas9 injection:protein\|FISH id:P2\|organ:right eye\|sorted plates:1	P2 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:right eye\|sorted plates:1	GSM3065990	GSM3065990: P2 right eye Scar; Danio rerio; RNA Seq	GSM3065990	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065990	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-Eye-right-p01-Scar_R1.fastq.gz P2-Eye-right-p01-Scar_R2.fastq.gz	fastq fastq	39029616.0	257084.0	GSM3065990 r1	0:75.94 1:75.88	A:7556894;C:11070936;G:13942796;T:6447595;N:11395	75	75	7556894	11070936	13942796	6447595	11395	SRX3839384	SRS3086672	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00367	0.00526	0.00323	0.00449	0.9988	0.99813	0.31168	0.32231	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Eye	Sensory System
43471	43471	SRR6888833	SRX3839383	SRS3086669	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 left eye Scar	GSM3065989	tissue:left eye single cells\|cas9 injection:protein\|FISH id:P2\|organ:left eye\|sorted plates:1	P2 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:left eye\|sorted plates:1	GSM3065989	GSM3065989: P2 left eye Scar; Danio rerio; RNA Seq	GSM3065989	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065989	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-Eye-left-p01-Scar_R2.fastq.gz P2-Eye-left-p01-Scar_R1.fastq.gz	fastq fastq	38948398.0	256405.0	GSM3065989 r1	0:75.98 1:75.92	A:7098142;C:11543244;G:14180784;T:6112258;N:13970	75	75	7098142	11543244	14180784	6112258	13970	SRX3839383	SRS3086669	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00055	0.00086	0.00048	0.00075	0.99979	0.99971	0.63636	0.375	75	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Eye	Sensory System
43472	43472	SRR6888831	SRX3839382	SRS3086668	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 cfin vent Scar	GSM3065988	tissue:primary fin single cells\|cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	P2 cfin vent Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	GSM3065988	GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq	GSM3065988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-CFin-Vent-003-Scar_R1.fastq.gz P2-CFin-Vent-003-Scar_R2.fastq.gz	fastq fastq	344793287.0	2269321.0	GSM3065988 r1	0:75.99 1:75.95	A:61565924;C:101344805;G:127059615;T:54785853;N:37090	75	75	61565924	101344805	127059615	54785853	37090	SRX3839382	SRS3086668	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	0.00029	0.00012	0.00017	0.99993	0.99977	0.33333	0.58823	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Fin	Surface Structure
43473	43473	SRR6888832	SRX3839382	SRS3086668	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P2 cfin vent Scar	GSM3065988	tissue:primary fin single cells\|cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	P2 cfin vent Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	GSM3065988	GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq	GSM3065988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz	fastq fastq	110701966.0	728490.0	GSM3065988 r2	0:75.99 1:75.97	A:19507928;C:32552811;G:40930271;T:17699467;N:11489	75	75	19507928	32552811	40930271	17699467	11489	SRX3839382	SRS3086668	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00021	0.0004	0.00015	0.00031	0.99991	0.99981	1.0	0.84615	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Fin	Surface Structure
43474	43474	SRR6888829	SRX3839381	SRS3086670	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P1 cfin dorsal Scar	GSM3065987	tissue:primary fin single cells\|cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	P1 cfin dorsal Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	GSM3065987	GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq	GSM3065987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-CFin-Dors-003-Scar_R2.fastq.gz P2-CFin-Dors-003-Scar_R1.fastq.gz	fastq fastq	537943644.0	3539989.0	GSM3065987 r1	0:75.99 1:75.97	A:94708808;C:157878001;G:198461680;T:86838061;N:57094	75	75	94708808	157878001	198461680	86838061	57094	SRX3839381	SRS3086670	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00016	0.00102	0.0001	0.00067	0.99995	0.99995	0.0	1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Fin	Surface Structure
43475	43475	SRR6888830	SRX3839381	SRS3086670	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	P1 cfin dorsal Scar	GSM3065987	tissue:primary fin single cells\|cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	P1 cfin dorsal Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:protein\|FISH id:P2\|organ:primary fin\|sorted plates:2	GSM3065987	GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq	GSM3065987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM3065987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz	fastq fastq	856597590.0	5637115.0	GSM3065987 r2	0:75.99 1:75.97	A:151359975;C:251587454;G:317011744;T:136549208;N:89209	75	75	151359975	251587454	317011744	136549208	89209	SRX3839381	SRS3086670	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00027	0.00065	0.00016	0.00039	0.99975	0.99951	0.29411	0.53658	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2018-03-23	Undetermined	Multi-stage	Fin	Surface Structure
43476	43476	SRR6020446	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p01_R1.fastq.gz R5_sec_Trans_p01_R2.fastq.gz	fastq fastq	5031589058.0	33202740.0	GSM2776988 r1	0:75.79 1:75.75	A:1144328847;C:1211156155;G:1480041764;T:1195826451;N:235841	75	75	1144328847	1211156155	1480041764	1195826451	235841	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.11853	0.24563	0.10636	0.21925	0.96585	0.92555	0.49894	0.48592	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43477	43477	SRR6020447	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p02_R2.fastq.gz R5_sec_Trans_p02_R1.fastq.gz	fastq fastq	5020749563.0	33189212.0	GSM2776988 r2	0:75.66 1:75.61	A:1271180542;C:1081665590;G:1257183505;T:1410487545;N:232381	75	75	1271180542	1081665590	1257183505	1410487545	232381	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.12477	0.33055	0.10671	0.26254	0.96773	0.90583	0.50071	0.48529	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43478	43478	SRR6020448	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p03_R1.fastq.gz R5_sec_Trans_p03_R2.fastq.gz	fastq fastq	9930849737.0	65769125.0	GSM2776988 r3	0:75.49 1:75.50	A:2771601461;C:1594447174;G:1778419273;T:3786066213;N:315616	75	75	2771601461	1594447174	1778419273	3786066213	315616	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.31895	0.74881	0.28344	0.57326	0.96546	0.85234	0.4987	0.52017	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43479	43479	SRR6020449	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p04_R1.fastq.gz R5_sec_Trans_p04_R2.fastq.gz	fastq fastq	7297925579.0	48343134.0	GSM2776988 r4	0:75.51 1:75.45	A:2157432534;C:1129186071;G:1200823243;T:2810444585;N:39146	75	75	2157432534	1129186071	1200823243	2810444585	39146	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.352	0.75293	0.31357	0.60441	0.95828	0.83885	0.50134	0.50535	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43480	43480	SRR6020450	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p05_R2.fastq.gz R5_sec_Trans_p05_R1.fastq.gz	fastq fastq	13855953318.0	91804628.0	GSM2776988 r5	0:75.50 1:75.43	A:4146316683;C:2217362039;G:2391706547;T:5100492721;N:75328	75	75	4146316683	2217362039	2391706547	5100492721	75328	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.37449	0.68646	0.32985	0.54102	0.95347	0.849	0.49416	0.50708	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43481	43481	SRR6020451	SRX3171493	SRS2501302	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Trans	GSM2776988	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776988	GSM2776988: R5 sec Trans; Danio rerio; RNA Seq	GSM2776988	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Trans_p06_R1.fastq.gz R5_sec_Trans_p06_R2.fastq.gz	fastq fastq	9723577592.0	64415623.0	GSM2776988 r6	0:75.50 1:75.45	A:2835431401;C:1511580093;G:1616039076;T:3760473139;N:53883	75	75	2835431401	1511580093	1616039076	3760473139	53883	SRX3171493	SRS2501302	SRA602108	GEO	AVO, Hubrecht Institue	2	0.33655	0.77492	0.29229	0.58155	0.95978	0.8454	0.49546	0.51051	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43482	43482	SRR6020440	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p01_R1.fastq.gz R5_sec_Scar_p01_R2.fastq.gz	fastq fastq	361194076.0	2376599.0	GSM2776987 r1	0:75.99 1:75.99	A:63932353;C:105212754;G:137339472;T:54692604;N:16893	75	75	63932353	105212754	137339472	54692604	16893	SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	7e-05	0.00012	4e-05	9e-05	0.99993	0.99991	0.5	0.75	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43483	43483	SRR6020441	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p02_R1.fastq.gz R5_sec_Scar_p02_R2.fastq.gz	fastq fastq	460055993.0	3027108.0	GSM2776987 r2	0:75.99 1:75.99	A:80579341;C:134185300;G:175364991;T:69904520;N:21841	75	75	80579341	134185300	175364991	69904520	21841	SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	5e-05	2e-05	2e-05	0.0	0.99997	0.99997	0.0	1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43484	43484	SRR6020442	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p03_R1.fastq.gz R5_sec_Scar_p03_R2.fastq.gz	fastq fastq	466000423.0	3066554.0	GSM2776987 r3	0:75.98 1:75.98	A:81301391;C:136221817;G:177874701;T:70591092;N:11422	75	75	81301391	136221817	177874701	70591092	11422	SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0001	0.00016	8e-05	0.00011	0.99993	0.99987	0.0	0.66666	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43485	43485	SRR6020443	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p04_R1.fastq.gz R5_sec_Scar_p04_R2.fastq.gz	fastq fastq	203843839.0	1341388.0	GSM2776987 r4										SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00013	0.00027	9e-05	0.00019	0.99995	0.99977	0.16666	0.66666	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43486	43486	SRR6020444	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p05_R1.fastq.gz R5_sec_Scar_p05_R2.fastq.gz	fastq fastq	305866297.0	2012742.0	GSM2776987 r5	0:75.98 1:75.98	A:53459692;C:89448285;G:116312720;T:46644195;N:1405	75	75	53459692	89448285	116312720	46644195	1405	SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	6e-05	9e-05	3e-05	5e-05	0.99997	0.99993	0.0	0.5	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43487	43487	SRR6020445	SRX3171492	SRS2501301	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 sec Scar	GSM2776987	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	R5 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:secondary fin\|sorted plates:6	GSM2776987	GSM2776987: R5 sec Scar; Danio rerio; RNA Seq	GSM2776987	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_sec_Scar_p06_R1.fastq.gz R5_sec_Scar_p06_R2.fastq.gz	fastq fastq	557494800.0	3670391.0	GSM2776987 r6	0:75.96 1:75.93	A:101252524;C:160223186;G:205832526;T:90183664;N:2900	75	75	101252524	160223186	205832526	90183664	2900	SRX3171492	SRS2501301	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00382	0.00768	0.00317	0.00636	0.99827	0.99673	0.48648	0.5	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43488	43488	SRR6020435	SRX3171491	SRS2501300	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Trans	GSM2776986	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	R5 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	GSM2776986	GSM2776986: R5 prim Trans; Danio rerio; RNA Seq	GSM2776986	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Trans_p02_R1.fastq.gz R5_prim_Trans_p02_R2.fastq.gz	fastq fastq	7812360278.0	51697480.0	GSM2776986 r1	0:75.54 1:75.58	A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950	75	75	2098454376	1641311761	1943503636	2128270555	819950	SRX3171491	SRS2501300	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01048	0.02593	0.00847	0.02007	0.99614	0.98742	0.33227	0.53419	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43489	43489	SRR6020436	SRX3171491	SRS2501300	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Trans	GSM2776986	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	R5 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	GSM2776986	GSM2776986: R5 prim Trans; Danio rerio; RNA Seq	GSM2776986	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Trans_p03_R1.fastq.gz R5_prim_Trans_p03_R2.fastq.gz	fastq fastq	6704494628.0	44436630.0	GSM2776986 r2	0:75.49 1:75.39	A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167	75	75	2087008571	1124579474	1252171872	2240541544	193167	SRX3171491	SRS2501300	SRA602108	GEO	AVO, Hubrecht Institue	2	0.24966	0.47946	0.21997	0.40259	0.95162	0.89191	0.48641	0.54514	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43490	43490	SRR6020437	SRX3171491	SRS2501300	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Trans	GSM2776986	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	R5 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	GSM2776986	GSM2776986: R5 prim Trans; Danio rerio; RNA Seq	GSM2776986	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Trans_p04_R1.fastq.gz R5_prim_Trans_p04_R2.fastq.gz	fastq fastq	8402262674.0	55692887.0	GSM2776986 r3	0:75.48 1:75.39	A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856	75	75	2618499207	1444061167	1613776766	2725680678	244856	SRX3171491	SRS2501300	SRA602108	GEO	AVO, Hubrecht Institue	2	0.26079	0.43317	0.23304	0.36897	0.95686	0.90575	0.50825	0.53432	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43491	43491	SRR6020438	SRX3171491	SRS2501300	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Trans	GSM2776986	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	R5 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	GSM2776986	GSM2776986: R5 prim Trans; Danio rerio; RNA Seq	GSM2776986	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Trans_p07_R1.fastq.gz R5_prim_Trans_p07_R2.fastq.gz	fastq fastq	7045442122.0	46667895.0	GSM2776986 r4	0:75.65 1:75.32	A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774	75	75	1992737539	1481998828	1584855122	1984679859	1170774	SRX3171491	SRS2501300	SRA602108	GEO	AVO, Hubrecht Institue	2	0.08866	0.20939	0.07714	0.18048	0.97906	0.95674	0.50746	0.52807	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43492	43492	SRR6020439	SRX3171491	SRS2501300	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Trans	GSM2776986	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	R5 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:5	GSM2776986	GSM2776986: R5 prim Trans; Danio rerio; RNA Seq	GSM2776986	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Trans_p08_R1.fastq.gz R5_prim_Trans_p08_R2.fastq.gz	fastq fastq	18530449971.0	122665653.0	GSM2776986 r5	0:75.68 1:75.38	A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121	75	75	4667348302	4333487274	4681098112	4848415162	101121	SRX3171491	SRS2501300	SRA602108	GEO	AVO, Hubrecht Institue	2	0.05599	0.12252	0.04627	0.10255	0.98409	0.96467	0.50898	0.5274	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43493	43493	SRR6020429	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p01_R1.fastq.gz R5_prim_Scar_p01_R2.fastq.gz	fastq fastq	24766319.0	163126.0	GSM2776985 r1	0:75.95 1:75.87	A:4693411;C:6959422;G:8727578;T:4381992;N:3916	75	75	4693411	6959422	8727578	4381992	3916	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00023	0.00064	0.00018	0.00044	0.99989	0.99969	0.6	0.8	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43494	43494	SRR6020430	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p02_R1.fastq.gz R5_prim_Scar_p02_R2.fastq.gz	fastq fastq	1266120923.0	8332017.0	GSM2776985 r2	0:75.98 1:75.98	A:222649072;C:369728088;G:482809574;T:190903334;N:30855	75	75	222649072	369728088	482809574	190903334	30855	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	4e-05	2e-05	3e-05	1e-05	0.99997	0.99997	0.0	1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43495	43495	SRR6020431	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p03_R1.fastq.gz R5_prim_Scar_p03_R2.fastq.gz	fastq fastq	494949145.0	3257351.0	GSM2776985 r3	0:75.98 1:75.97	A:87163836;C:143707892;G:188542837;T:75522642;N:11938	75	75	87163836	143707892	188542837	75522642	11938	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	5e-05	9e-05	2e-05	0.99995	0.99993	0.0	0.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43496	43496	SRR6020432	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p04_R1.fastq.gz R5_prim_Scar_p04_R2.fastq.gz	fastq fastq	376701290.0	2478856.0	GSM2776985 r4	0:75.99 1:75.98	A:66002492;C:109979363;G:143811826;T:56905698;N:1911	75	75	66002492	109979363	143811826	56905698	1911	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	4e-05	5e-05	3e-05	4e-05	1.0	1.0			76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43497	43497	SRR6020433	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p07_R1.fastq.gz R5_prim_Scar_p07_R2.fastq.gz	fastq fastq	34956996.0	230152.0	GSM2776985 r5	0:75.96 1:75.92	A:6443422;C:10072498;G:12853211;T:5583477;N:4388	75	75	6443422	10072498	12853211	5583477	4388	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00459	0.01152	0.00401	0.00964	0.99821	0.99624	0.43333	0.53588	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43498	43498	SRR6020434	SRX3171490	SRS2501299	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R5 prim Scar	GSM2776985	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	R5 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R5\|tissue:primary fin\|sorted plates:6	GSM2776985	GSM2776985: R5 prim Scar; Danio rerio; RNA Seq	GSM2776985	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R5_prim_Scar_p08_R1.fastq.gz R5_prim_Scar_p08_R2.fastq.gz	fastq fastq	833299107.0	5483661.0	GSM2776985 r6	0:75.98 1:75.98	A:145414972;C:243570136;G:319061924;T:125238697;N:13378	75	75	145414972	243570136	319061924	125238697	13378	SRX3171490	SRS2501299	SRA602108	GEO	AVO, Hubrecht Institue	2	6e-05	8e-05	2e-05	3e-05	0.99991	0.99989	0.75	0.8	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43499	43499	SRR6020425	SRX3171489	SRS2501298	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Trans	GSM2776984	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776984	GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq	GSM2776984	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776984	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Trans_p01_R1.fastq.gz R4_wkm_Trans_p01_R2.fastq.gz	fastq fastq	3927170013.0	26023917.0	GSM2776984 r1	0:75.41 1:75.50	A:1129996659;C:572501533;G:611837437;T:1612813099;N:21285	75	75	1129996659	572501533	611837437	1612813099	21285	SRX3171489	SRS2501298	SRA602108	GEO	AVO, Hubrecht Institue	2	0.32239	0.87342	0.20343	0.36809	0.95722	0.82919	0.49895	0.48491	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43500	43500	SRR6020426	SRX3171489	SRS2501298	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Trans	GSM2776984	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776984	GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq	GSM2776984	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776984	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Trans_p02_R1.fastq.gz R4_wkm_Trans_p02_R2.fastq.gz	fastq fastq	4030497815.0	26709253.0	GSM2776984 r2	0:75.41 1:75.49	A:1162066088;C:581519292;G:627111524;T:1659778815;N:22096	75	75	1162066088	581519292	627111524	1659778815	22096	SRX3171489	SRS2501298	SRA602108	GEO	AVO, Hubrecht Institue	2	0.33073	0.87349	0.21896	0.35721	0.96337	0.82895	0.48607	0.49848	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43501	43501	SRR6020427	SRX3171489	SRS2501298	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Trans	GSM2776984	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776984	GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq	GSM2776984	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776984	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Trans_p03_R1.fastq.gz R4_wkm_Trans_p03_R2.fastq.gz	fastq fastq	3631053942.0	24060145.0	GSM2776984 r3	0:75.46 1:75.46	A:1043256309;C:532046798;G:537476503;T:1518171924;N:102408	75	75	1043256309	532046798	537476503	1518171924	102408	SRX3171489	SRS2501298	SRA602108	GEO	AVO, Hubrecht Institue	2	0.32814	0.80344	0.24082	0.39956	0.96319	0.85831	0.49813	0.5276	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43502	43502	SRR6020428	SRX3171489	SRS2501298	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Trans	GSM2776984	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776984	GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq	GSM2776984	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776984	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Trans_p04_R1.fastq.gz R4_wkm_Trans_p04_R2.fastq.gz	fastq fastq	4828053523.0	31991602.0	GSM2776984 r4	0:75.42 1:75.50	A:1401132307;C:703203743;G:750174359;T:1973515875;N:27239	75	75	1401132307	703203743	750174359	1973515875	27239	SRX3171489	SRS2501298	SRA602108	GEO	AVO, Hubrecht Institue	2	0.3505	0.86169	0.26499	0.42336	0.96027	0.8182	0.49142	0.49842	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43503	43503	SRR6020421	SRX3171488	SRS2501297	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Scar	GSM2776983	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776983	GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq	GSM2776983	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776983	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Scar_p01_R1.fastq.gz R4_wkm_Scar_p01_R2.fastq.gz	fastq fastq	614245655.0	4041684.0	GSM2776983 r1	0:75.99 1:75.99	A:107048177;C:178914249;G:231725646;T:96554319;N:3264	75	75	107048177	178914249	231725646	96554319	3264	SRX3171488	SRS2501297	SRA602108	GEO	AVO, Hubrecht Institue	2	4e-05	0.00013	1e-05	8e-05	0.99997	0.99991	1.0	0.875	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43504	43504	SRR6020422	SRX3171488	SRS2501297	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Scar	GSM2776983	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776983	GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq	GSM2776983	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776983	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Scar_p02_R1.fastq.gz R4_wkm_Scar_p02_R2.fastq.gz	fastq fastq	817459087.0	5378786.0	GSM2776983 r2	0:75.99 1:75.99	A:143806910;C:238933705;G:307736025;T:126978347;N:4100	75	75	143806910	238933705	307736025	126978347	4100	SRX3171488	SRS2501297	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	4e-05	1e-05	1e-05	0.99995	0.99995	0.5	0.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43505	43505	SRR6020423	SRX3171488	SRS2501297	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Scar	GSM2776983	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776983	GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq	GSM2776983	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776983	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Scar_p03_R1.fastq.gz R4_wkm_Scar_p03_R2.fastq.gz	fastq fastq	3981890019.0	26204072.0	GSM2776983 r3	0:75.98 1:75.97	A:703462533;C:1148861227;G:1510546877;T:618921234;N:98148	75	75	703462533	1148861227	1510546877	618921234	98148	SRX3171488	SRS2501297	SRA602108	GEO	AVO, Hubrecht Institue	2	7e-05	9e-05	4e-05	4e-05	0.99993	0.99987	0.25	0.42857	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43506	43506	SRR6020424	SRX3171488	SRS2501297	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 wkm Scar	GSM2776983	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	R4 wkm Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	wkm single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:whole kidney marrow\|sorted plates:4	GSM2776983	GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq	GSM2776983	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776983	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_wkm_Scar_p04_R1.fastq.gz R4_wkm_Scar_p04_R2.fastq.gz	fastq fastq	561112602.0	3692109.0	GSM2776983 r4	0:75.98 1:75.99	A:98682129;C:162936789;G:209922290;T:89568564;N:2830	75	75	98682129	162936789	209922290	89568564	2830	SRX3171488	SRS2501297	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00016	9e-05	4e-05	5e-05	0.99973	0.99993	0.72727	0.75	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Kidney	Renal System
43507	43507	SRR6020417	SRX3171487	SRS2501295	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Trans	GSM2776982	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776982	GSM2776982: R4 terv Trans; Danio rerio; RNA Seq	GSM2776982	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776982	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Trans_p01_R1.fastq.gz R4_terv_Trans_p01_R2.fastq.gz	fastq fastq	899878376.0	5966262.0	GSM2776982 r1	0:75.45 1:75.38	A:292042567;C:146271033;G:139925382;T:321623997;N:15397	75	75	292042567	146271033	139925382	321623997	15397	SRX3171487	SRS2501295	SRA602108	GEO	AVO, Hubrecht Institue	2	0.33677	0.59727	0.29432	0.51752	0.95641	0.92176	0.48959	0.52071	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43508	43508	SRR6020418	SRX3171487	SRS2501295	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Trans	GSM2776982	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776982	GSM2776982: R4 terv Trans; Danio rerio; RNA Seq	GSM2776982	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776982	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Trans_p02_R2.fastq.gz R4_terv_Trans_p02_R1.fastq.gz	fastq fastq	8835694041.0	58517949.0	GSM2776982 r2	0:75.51 1:75.48	A:2524661133;C:1502485662;G:1635422368;T:3172516743;N:608135	75	75	2524661133	1502485662	1635422368	3172516743	608135	SRX3171487	SRS2501295	SRA602108	GEO	AVO, Hubrecht Institue	2	0.37169	0.69933	0.33104	0.59253	0.93659	0.82836	0.49319	0.51176	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43509	43509	SRR6020419	SRX3171487	SRS2501295	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Trans	GSM2776982	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776982	GSM2776982: R4 terv Trans; Danio rerio; RNA Seq	GSM2776982	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776982	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Trans_p03_R1.fastq.gz R4_terv_Trans_p03_R2.fastq.gz	fastq fastq	4386400893.0	29067702.0	GSM2776982 r3	0:75.49 1:75.41	A:1326956065;C:724491767;G:749677156;T:1585148439;N:127466	75	75	1326956065	724491767	749677156	1585148439	127466	SRX3171487	SRS2501295	SRA602108	GEO	AVO, Hubrecht Institue	2	0.31136	0.62851	0.26305	0.46553	0.95517	0.87024	0.52178	0.52923	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43510	43510	SRR6020420	SRX3171487	SRS2501295	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Trans	GSM2776982	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776982	GSM2776982: R4 terv Trans; Danio rerio; RNA Seq	GSM2776982	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776982	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Trans_p04_R1.fastq.gz R4_terv_Trans_p04_R2.fastq.gz	fastq fastq	9245152121.0	61263899.0	GSM2776982 r4	0:75.46 1:75.45	A:2833957542;C:1482543934;G:1582652549;T:3345945412;N:52684	75	75	2833957542	1482543934	1582652549	3345945412	52684	SRX3171487	SRS2501295	SRA602108	GEO	AVO, Hubrecht Institue	2	0.33283	0.69016	0.28123	0.49239	0.95039	0.83437	0.49598	0.54367	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43511	43511	SRR6020413	SRX3171486	SRS2501296	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Scar	GSM2776981	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776981	GSM2776981: R4 terv Scar; Danio rerio; RNA Seq	GSM2776981	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Scar_p01_R1.fastq.gz R4_terv_Scar_p01_R2.fastq.gz	fastq fastq	63013537.0	414730.0	GSM2776981 r1	0:75.98 1:75.96	A:11340679;C:18348371;G:23382873;T:9940711;N:903	75	75	11340679	18348371	23382873	9940711	903	SRX3171486	SRS2501296	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0005	0.0001	0.00026	7e-05	0.99993	0.99995	0.05882	1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43512	43512	SRR6020414	SRX3171486	SRS2501296	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Scar	GSM2776981	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776981	GSM2776981: R4 terv Scar; Danio rerio; RNA Seq	GSM2776981	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Scar_p02_R1.fastq.gz R4_terv_Scar_p02_R2.fastq.gz	fastq fastq	118778173.0	782191.0	GSM2776981 r2	0:75.93 1:75.92	A:22484503;C:33087570;G:42161784;T:21035442;N:8874	75	75	22484503	33087570	42161784	21035442	8874	SRX3171486	SRS2501296	SRA602108	GEO	AVO, Hubrecht Institue	2	0.02075	0.05067	0.01832	0.04276	0.99279	0.97654	0.44392	0.52218	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43513	43513	SRR6020415	SRX3171486	SRS2501296	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Scar	GSM2776981	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776981	GSM2776981: R4 terv Scar; Danio rerio; RNA Seq	GSM2776981	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Scar_p03_R1.fastq.gz R4_terv_Scar_p03_R2.fastq.gz	fastq fastq	713249164.0	4694227.0	GSM2776981 r3	0:75.98 1:75.96	A:125818684;C:207435216;G:268732472;T:111244414;N:18378	75	75	125818684	207435216	268732472	111244414	18378	SRX3171486	SRS2501296	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	1e-05	1e-05	0.0	0.99997	1.0	0.0		76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43514	43514	SRR6020416	SRX3171486	SRS2501296	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terv Scar	GSM2776981	source name:tertiary ventral fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terv Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary ventral fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776981	GSM2776981: R4 terv Scar; Danio rerio; RNA Seq	GSM2776981	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terv_Scar_p04_R1.fastq.gz R4_terv_Scar_p04_R2.fastq.gz	fastq fastq	483844486.0	3184595.0	GSM2776981 r4	0:75.98 1:75.95	A:85646205;C:140894435;G:180981122;T:76320328;N:2396	75	75	85646205	140894435	180981122	76320328	2396	SRX3171486	SRS2501296	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0003	0.00067	0.00018	0.00046	0.99989	0.99935	0.15	0.41176	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43515	43515	SRR6020409	SRX3171485	SRS2501294	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Trans	GSM2776980	source name:tertiary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776980	GSM2776980: R4 terd Trans; Danio rerio; RNA Seq	GSM2776980	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Trans_p01_R1.fastq.gz R4_terd_Trans_p01_R2.fastq.gz	fastq fastq	9353477829.0	61985103.0	GSM2776980 r1	0:75.45 1:75.45	A:2918476093;C:1414091678;G:1474868294;T:3545988622;N:53142	75	75	2918476093	1414091678	1474868294	3545988622	53142	SRX3171485	SRS2501294	SRA602108	GEO	AVO, Hubrecht Institue	2	0.36441	0.7593	0.31336	0.55295	0.95093	0.82292	0.49914	0.53019	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43516	43516	SRR6020410	SRX3171485	SRS2501294	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Trans	GSM2776980	source name:tertiary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776980	GSM2776980: R4 terd Trans; Danio rerio; RNA Seq	GSM2776980	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Trans_p02_R1.fastq.gz R4_terd_Trans_p02_R2.fastq.gz	fastq fastq	6626365664.0	43908545.0	GSM2776980 r2	0:75.44 1:75.47	A:1980665411;C:1019945066;G:1082628078;T:2543089101;N:38008	75	75	1980665411	1019945066	1082628078	2543089101	38008	SRX3171485	SRS2501294	SRA602108	GEO	AVO, Hubrecht Institue	2	0.32749	0.78639	0.25705	0.43545	0.95745	0.82	0.5	0.52298	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43517	43517	SRR6020411	SRX3171485	SRS2501294	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Trans	GSM2776980	source name:tertiary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776980	GSM2776980: R4 terd Trans; Danio rerio; RNA Seq	GSM2776980	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Trans_p03_R1.fastq.gz R4_terd_Trans_p03_R2.fastq.gz	fastq fastq	250213383.0	1657189.0	GSM2776980 r3	0:75.51 1:75.48	A:70872645;C:40721033;G:44641734;T:93961355;N:16616	75	75	70872645	40721033	44641734	93961355	16616	SRX3171485	SRS2501294	SRA602108	GEO	AVO, Hubrecht Institue	2	0.39985	0.75081	0.34725	0.58284	0.93975	0.82116	0.49709	0.51312	76	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43518	43518	SRR6020412	SRX3171485	SRS2501294	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Trans	GSM2776980	source name:tertiary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	tertiary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776980	GSM2776980: R4 terd Trans; Danio rerio; RNA Seq	GSM2776980	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Trans_p04_R1.fastq.gz R4_terd_Trans_p04_R2.fastq.gz	fastq fastq	2439737928.0	16175327.0	GSM2776980 r4	0:75.43 1:75.40	A:791363066;C:393366804;G:387269134;T:867699009;N:39915	75	75	791363066	393366804	387269134	867699009	39915	SRX3171485	SRS2501294	SRA602108	GEO	AVO, Hubrecht Institue	2	0.41064	0.68389	0.36279	0.60184	0.94801	0.91321	0.50483	0.5018	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43519	43519	SRR6020405	SRX3171484	SRS2501293	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Scar	GSM2776979	source name:teritary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	teritary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776979	GSM2776979: R4 terd Scar; Danio rerio; RNA Seq	GSM2776979	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776979	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Scar_p01_R1.fastq.gz R4_terd_Scar_p01_R2.fastq.gz	fastq fastq	472339159.0	3108723.0	GSM2776979 r1	0:75.98 1:75.96	A:83061434;C:137317024;G:178719638;T:73238676;N:2387	75	75	83061434	137317024	178719638	73238676	2387	SRX3171484	SRS2501293	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00033	0.00025	0.0002	0.00013	0.99993	0.99963	0.0	0.61111	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43520	43520	SRR6020406	SRX3171484	SRS2501293	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Scar	GSM2776979	source name:teritary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	teritary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776979	GSM2776979: R4 terd Scar; Danio rerio; RNA Seq	GSM2776979	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776979	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Scar_p02_R1.fastq.gz R4_terd_Scar_p02_R2.fastq.gz	fastq fastq	405913408.0	2671239.0	GSM2776979 r2	0:75.99 1:75.97	A:71703296;C:117980100;G:153764667;T:62463222;N:2123	75	75	71703296	117980100	153764667	62463222	2123	SRX3171484	SRS2501293	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	0.00011	1e-05	4e-05	0.99993	0.99981	0.66666	0.7	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43521	43521	SRR6020407	SRX3171484	SRS2501293	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Scar	GSM2776979	source name:teritary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	teritary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776979	GSM2776979: R4 terd Scar; Danio rerio; RNA Seq	GSM2776979	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776979	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Scar_p03_R1.fastq.gz R4_terd_Scar_p03_R2.fastq.gz	fastq fastq	35300008.0	232328.0	GSM2776979 r3	0:75.97 1:75.97	A:6443488;C:10004950;G:13144621;T:5704811;N:2138	75	75	6443488	10004950	13144621	5704811	2138	SRX3171484	SRS2501293	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00275	0.00097	0.00214	0.00083	0.99943	0.99955	0.15454	0.52173	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43522	43522	SRR6020408	SRX3171484	SRS2501293	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 terd Scar	GSM2776979	source name:teritary dorsal fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	R4 terd Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	teritary dorsal fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:tertiary fin\|sorted plates:4	GSM2776979	GSM2776979: R4 terd Scar; Danio rerio; RNA Seq	GSM2776979	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776979	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_terd_Scar_p04_R1.fastq.gz R4_terd_Scar_p04_R2.fastq.gz	fastq fastq	35300008.0	232328.0	GSM2776979 r4	0:75.97 1:75.97	A:6443488;C:10004950;G:13144621;T:5704811;N:2138	75	75	6443488	10004950	13144621	5704811	2138	SRX3171484	SRS2501293	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00276	0.00097	0.00213	0.00082	0.99945	0.99949	0.14035	0.53846	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43523	43523	SRR6020399	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p01_R1.fastq.gz R4_sec_Trans_p01_R2.fastq.gz	fastq fastq	7943223694.0	52632584.0	GSM2776978 r1	0:75.50 1:75.42	A:2426047253;C:1345760701;G:1411992441;T:2757726644;N:1696655	75	75	2426047253	1345760701	1411992441	2757726644	1696655	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.39936	0.64405	0.35361	0.55608	0.91311	0.84431	0.5165	0.52376	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43524	43524	SRR6020400	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p02_R1.fastq.gz R4_sec_Trans_p02_R2.fastq.gz	fastq fastq	8875571511.0	58802279.0	GSM2776978 r2	0:75.52 1:75.42	A:2702312372;C:1527849144;G:1608513066;T:3034988415;N:1908514	75	75	2702312372	1527849144	1608513066	3034988415	1908514	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.38955	0.61673	0.34428	0.5327	0.91774	0.85094	0.50279	0.51953	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43525	43525	SRR6020401	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p03_R1.fastq.gz R4_sec_Trans_p03_R2.fastq.gz	fastq fastq	10196306186.0	67549716.0	GSM2776978 r3	0:75.48 1:75.47	A:3021055822;C:1591602601;G:1717130650;T:3866184067;N:333046	75	75	3021055822	1591602601	1717130650	3866184067	333046	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.42177	0.73274	0.37881	0.60342	0.93845	0.83104	0.49961	0.48288	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43526	43526	SRR6020402	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p04_R1.fastq.gz R4_sec_Trans_p04_R2.fastq.gz	fastq fastq	16321632703.0	108129317.0	GSM2776978 r4	0:75.48 1:75.47	A:4839288181;C:2524952022;G:2722722795;T:6234157991;N:511714	75	75	4839288181	2524952022	2722722795	6234157991	511714	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.43062	0.74617	0.38255	0.59574	0.93693	0.8256	0.50653	0.53888	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43527	43527	SRR6020403	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p05_R1.fastq.gz R4_sec_Trans_p05_R2.fastq.gz	fastq fastq	8368447970.0	55444521.0	GSM2776978 r5	0:75.47 1:75.46	A:2470524458;C:1322545235;G:1459320910;T:3115796506;N:260861	75	75	2470524458	1322545235	1459320910	3115796506	260861	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.38066	0.70664	0.33844	0.56193	0.94134	0.82846	0.48774	0.47937	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43528	43528	SRR6020404	SRX3171483	SRS2501292	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Trans	GSM2776978	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776978	GSM2776978: R4 sec Trans; Danio rerio; RNA Seq	GSM2776978	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Trans_p06_R1.fastq.gz R4_sec_Trans_p06_R2.fastq.gz	fastq fastq	9774461624.0	64760766.0	GSM2776978 r6	0:75.47 1:75.46	A:2902527714;C:1488941576;G:1661506049;T:3721177113;N:309172	75	75	2902527714	1488941576	1661506049	3721177113	309172	SRX3171483	SRS2501292	SRA602108	GEO	AVO, Hubrecht Institue	2	0.39334	0.71354	0.35122	0.56253	0.94513	0.84628	0.47779	0.55996	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43529	43529	SRR6020393	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p01_R1.fastq.gz R4_sec_Scar_p01_R2.fastq.gz	fastq fastq	443752860.0	2921141.0	GSM2776977 r1	0:75.98 1:75.93	A:78584919;C:129545943;G:166851959;T:68680115;N:89924	75	75	78584919	129545943	166851959	68680115	89924	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00014	0.00018	9e-05	0.00013	0.99991	0.99985	0.4	0.57142	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43530	43530	SRR6020394	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p02_R1.fastq.gz R4_sec_Scar_p02_R2.fastq.gz	fastq fastq	609377510.0	4011701.0	GSM2776977 r2	0:75.99 1:75.91	A:108185883;C:176784326;G:229824363;T:94453370;N:129568	75	75	108185883	176784326	229824363	94453370	129568	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	6e-05	0.0001	5e-05	7e-05	1.0	0.99991		0.25	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43531	43531	SRR6020395	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p03_R1.fastq.gz R4_sec_Scar_p03_R2.fastq.gz	fastq fastq	695786067.0	4580703.0	GSM2776977 r3	0:75.98 1:75.91	A:122056429;C:202686271;G:262426973;T:108597814;N:18580	75	75	122056429	202686271	262426973	108597814	18580	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00035	0.00084	0.00028	0.00068	0.99981	0.99955	0.18181	0.45454	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43532	43532	SRR6020396	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p04_R1.fastq.gz R4_sec_Scar_p04_R2.fastq.gz	fastq fastq	468236053.0	3082347.0	GSM2776977 r4	0:75.98 1:75.92	A:82822403;C:136423938;G:175959465;T:73018299;N:11948	75	75	82822403	136423938	175959465	73018299	11948	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	7e-05	1e-05	3e-05	0.99997	0.99991	0.0	0.75	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43533	43533	SRR6020397	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p05_R1.fastq.gz R4_sec_Scar_p05_R2.fastq.gz	fastq fastq	494012269.0	3251619.0	GSM2776977 r5	0:75.98 1:75.94	A:87398485;C:143668568;G:186485697;T:76445953;N:13566	75	75	87398485	143668568	186485697	76445953	13566	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	8e-05	7e-05	4e-05	1e-05	0.99991	0.99985	0.2	0.71428	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43534	43534	SRR6020398	SRX3171482	SRS2501291	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 sec Scar	GSM2776977	source name:secondary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	R4 sec Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	secondary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:secondary fin\|sorted plates:6	GSM2776977	GSM2776977: R4 sec Scar; Danio rerio; RNA Seq	GSM2776977	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_sec_Scar_p06_R1.fastq.gz R4_sec_Scar_p06_R2.fastq.gz	fastq fastq	488664520.0	3216541.0	GSM2776977 r6	0:75.98 1:75.94	A:86623588;C:141946345;G:183757005;T:76325350;N:12232	75	75	86623588	141946345	183757005	76325350	12232	SRX3171482	SRS2501291	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0001	0.00015	5e-05	8e-05	0.99991	0.99983	0.16666	0.75	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43535	43535	SRR6020387	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p01_R1.fastq.gz R4_prim_Trans_p01_R2.fastq.gz	fastq fastq	4156649914.0	27498834.0	GSM2776976 r1	0:75.66 1:75.50	A:1184667722;C:812111779;G:946047137;T:1213491214;N:332062	75	75	1184667722	812111779	946047137	1213491214	332062	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.13191	0.27606	0.11079	0.21313	0.97981	0.95864	0.48952	0.51323	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43536	43536	SRR6020388	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p02_R1.fastq.gz R4_prim_Trans_p02_R2.fastq.gz	fastq fastq	5961095878.0	39431358.0	GSM2776976 r2	0:75.66 1:75.51	A:1678045732;C:1185915367;G:1391829821;T:1704836561;N:468397	75	75	1678045732	1185915367	1391829821	1704836561	468397	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.13017	0.27029	0.11004	0.21778	0.9795	0.95978	0.54044	0.51146	76	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43537	43537	SRR6020389	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p03_R1.fastq.gz R4_prim_Trans_p03_R2.fastq.gz	fastq fastq	6170232577.0	40846092.0	GSM2776976 r3	0:75.56 1:75.50	A:1866777846;C:1148020988;G:1151073641;T:2003993265;N:366837	75	75	1866777846	1148020988	1151073641	2003993265	366837	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.21204	0.40881	0.18286	0.33189	0.95931	0.9108	0.49141	0.53253	75	76	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43538	43538	SRR6020390	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p04_R1.fastq.gz R4_prim_Trans_p04_R2.fastq.gz	fastq fastq	11725606474.0	77611342.0	GSM2776976 r4	0:75.62 1:75.46	A:3255674293;C:2567072026;G:2847190480;T:3054954945;N:714730	75	75	3255674293	2567072026	2847190480	3054954945	714730	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.06986	0.13983	0.05982	0.11888	0.98516	0.97161	0.49686	0.4638	75	75	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43539	43539	SRR6020391	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p05_R1.fastq.gz R4_prim_Trans_p05_R2.fastq.gz	fastq fastq	10721896827.0	71080622.0	GSM2776976 r5	0:75.44 1:75.41	A:3568478635;C:1747554798;G:1675757438;T:3729472140;N:633816	75	75	3568478635	1747554798	1675757438	3729472140	633816	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.32298	0.52706	0.28009	0.43701	0.94349	0.90078	0.51345	0.52304	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43540	43540	SRR6020392	SRX3171481	SRS2501290	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Trans	GSM2776976	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776976	GSM2776976: R4 prim Trans; Danio rerio; RNA Seq	GSM2776976	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Trans_p06_R1.fastq.gz R4_prim_Trans_p06_R2.fastq.gz	fastq fastq	4861560177.0	32218130.0	GSM2776976 r6	0:75.46 1:75.44	A:1606516776;C:766379277;G:687731226;T:1800636189;N:296709	75	75	1606516776	766379277	687731226	1800636189	296709	SRX3171481	SRS2501290	SRA602108	GEO	AVO, Hubrecht Institue	2	0.40198	0.66219	0.35056	0.55779	0.94671	0.8913	0.48395	0.50179	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43541	43541	SRR6020381	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p01_R1.fastq.gz R4_prim_Scar_p01_R2.fastq.gz	fastq fastq	2115181733.0	13930610.0	GSM2776975 r1	0:75.96 1:75.88	A:379992687;C:608145647;G:806462037;T:320430832;N:150530	75	75	379992687	608145647	806462037	320430832	150530	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	4e-05	2e-05	2e-05	1.0	0.99997		1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43542	43542	SRR6020382	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p02_R1.fastq.gz R4_prim_Scar_p02_R2.fastq.gz	fastq fastq	1500850853.0	9884525.0	GSM2776975 r2	0:75.96 1:75.88	A:272764495;C:429257065;G:572879423;T:225831427;N:118443	75	75	272764495	429257065	572879423	225831427	118443	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0	3e-05	0.0	1e-05	1.0	0.99997		0.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43543	43543	SRR6020383	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p03_R1.fastq.gz R4_prim_Scar_p03_R2.fastq.gz	fastq fastq	1802726164.0	11867972.0	GSM2776975 r3	0:75.98 1:75.91	A:320691778;C:528568175;G:676214104;T:277152518;N:99589	75	75	320691778	528568175	676214104	277152518	99589	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	1e-05	0.0	0.0	0.0	1.0	1.0			76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43544	43544	SRR6020384	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p04_R1.fastq.gz R4_prim_Scar_p04_R2.fastq.gz	fastq fastq	1589218979.0	10459351.0	GSM2776975 r4	0:75.98 1:75.96	A:284759473;C:465370937;G:594649808;T:244354408;N:84353	75	75	284759473	465370937	594649808	244354408	84353	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	8e-05	2e-05	6e-05	0.99997	0.99997	0.0	1.0	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43545	43545	SRR6020385	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p05_R1.fastq.gz R4_prim_Scar_p05_R2.fastq.gz	fastq fastq	1044289567.0	6872484.0	GSM2776975 r5	0:75.99 1:75.97	A:180521535;C:302898685;G:398946567;T:161866241;N:56539	75	75	180521535	302898685	398946567	161866241	56539	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0	2e-05	0.0	1e-05	1.0	1.0			76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43546	43546	SRR6020386	SRX3171480	SRS2501289	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R4 prim Scar	GSM2776975	source name:primary fin single cells\|cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	R4 prim Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	primary fin single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R4\|tissue:primary fin\|sorted plates:6	GSM2776975	GSM2776975: R4 prim Scar; Danio rerio; RNA Seq	GSM2776975	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R4_prim_Scar_p06_R1.fastq.gz R4_prim_Scar_p06_R2.fastq.gz	fastq fastq	1191573683.0	7850142.0	GSM2776975 r6	0:75.98 1:75.81	A:222979447;C:342633187;G:444672356;T:181222920;N:65773	75	75	222979447	342633187	444672356	181222920	65773	SRX3171480	SRS2501289	SRA602108	GEO	AVO, Hubrecht Institue	2	3e-05	0.0	1e-05	0.0	0.99997	1.0	1.0		76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Fin	Surface Structure
43547	43547	SRR6020379	SRX3171479	SRS2501288	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right midbrain Trans	GSM2776974	source name:right midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	R3 right midbrain Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	GSM2776974	GSM2776974: R3 right midbrain Trans; Danio rerio; RNA Seq	GSM2776974	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776974	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-midbrain_Trans_p01_R1.fastq.gz R3_right-midbrain_Trans_p01_R2.fastq.gz	fastq fastq	7311568521.0	48480885.0	GSM2776974 r1	0:75.55 1:75.26	A:2546694537;C:1258523151;G:1288739506;T:2216373333;N:1237994	75	75	2546694537	1258523151	1288739506	2216373333	1237994	SRX3171479	SRS2501288	SRA602108	GEO	AVO, Hubrecht Institue	2	0.05784	0.23487	0.04345	0.14886	0.98559	0.9346	0.44607	0.47221	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43548	43548	SRR6020380	SRX3171479	SRS2501288	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right midbrain Trans	GSM2776974	source name:right midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	R3 right midbrain Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	GSM2776974	GSM2776974: R3 right midbrain Trans; Danio rerio; RNA Seq	GSM2776974	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776974	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-midbrain_Trans_p02_R1.fastq.gz R3_right-midbrain_Trans_p02_R2.fastq.gz	fastq fastq	5504663628.0	36469519.0	GSM2776974 r2	0:75.60 1:75.34	A:1821437650;C:1054551371;G:1113933940;T:1513827158;N:913509	75	75	1821437650	1054551371	1113933940	1513827158	913509	SRX3171479	SRS2501288	SRA602108	GEO	AVO, Hubrecht Institue	2	0.05795	0.17825	0.04288	0.11406	0.98305	0.94809	0.47968	0.45805	75	76	B	B	mate1-mate2 similar by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43549	43549	SRR6020377	SRX3171478	SRS2501285	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right midbrain Scar	GSM2776973	source name:right midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	R3 right midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	GSM2776973	GSM2776973: R3 right midbrain Scar; Danio rerio; RNA Seq	GSM2776973	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776973	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-midbrain_Scar_p01_R1.fastq.gz R3_right-midbrain_Scar_p01_R2.fastq.gz	fastq fastq	73161383.0	482327.0	GSM2776973 r1	0:75.96 1:75.73	A:14101004;C:20286175;G:24361525;T:14401926;N:10753	75	75	14101004	20286175	24361525	14401926	10753	SRX3171478	SRS2501285	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00066	0.00077	0.00046	0.00057	0.99981	0.99957	0.12903	0.60869	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43550	43550	SRR6020378	SRX3171478	SRS2501285	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right midbrain Scar	GSM2776973	source name:right midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	R3 right midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right midbrain\|sorted plates:2	GSM2776973	GSM2776973: R3 right midbrain Scar; Danio rerio; RNA Seq	GSM2776973	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776973	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-midbrain_Scar_p02_R1.fastq.gz R3_right-midbrain_Scar_p02_R2.fastq.gz	fastq fastq	72819701.0	479667.0	GSM2776973 r2	0:75.95 1:75.87	A:14035275;C:20415974;G:26137916;T:12219810;N:10726	75	75	14035275	20415974	26137916	12219810	10726	SRX3171478	SRS2501285	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00698	0.00375	0.00508	0.00229	0.99967	0.99711	0.02721	0.49677	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43551	43551	SRR6020376	SRX3171477	SRS2501287	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 left midbrain Trans	GSM2776972	source name:left midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:1	R3 left midbrain Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:1	GSM2776972	GSM2776972: R3 left midbrain Trans; Danio rerio; RNA Seq	GSM2776972	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776972	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_left-midbrain_Trans_p02_R2.fastq.gz R3_left-midbrain_Trans_p02_R1.fastq.gz	fastq fastq	17092068701.0	113381987.0	GSM2776972 r1	0:75.54 1:75.21	A:5993846073;C:3139834829;G:3385691310;T:4569832402;N:2864087	75	75	5993846073	3139834829	3385691310	4569832402	2864087	SRX3171477	SRS2501287	SRA602108	GEO	AVO, Hubrecht Institue	2	0.02415	0.07091	0.01797	0.04896	0.99644	0.98397	0.55523	0.57244	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43552	43552	SRR6020374	SRX3171476	SRS2501286	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 left midbrain Scar	GSM2776971	source name:left midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:2	R3 left midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:2	GSM2776971	GSM2776971: R3 left midbrain Scar; Danio rerio; RNA Seq	GSM2776971	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776971	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_left-midbrain_Scar_p01_R1.fastq.gz R3_left-midbrain_Scar_p01_R2.fastq.gz	fastq fastq	19197472.0	126382.0	GSM2776971 r1	0:75.98 1:75.92	A:3378587;C:5537697;G:7213721;T:3065479;N:1988	75	75	3378587	5537697	7213721	3065479	1988	SRX3171476	SRS2501286	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00097	0.00126	0.00084	0.00066	0.99991	0.99977	0.1	0.4	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43553	43553	SRR6020375	SRX3171476	SRS2501286	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 left midbrain Scar	GSM2776971	source name:left midbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:2	R3 left midbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left midbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:left midbrain\|sorted plates:2	GSM2776971	GSM2776971: R3 left midbrain Scar; Danio rerio; RNA Seq	GSM2776971	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776971	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_left-midbrain_Scar_p02_R1.fastq.gz R3_left-midbrain_Scar_p02_R2.fastq.gz	fastq fastq	17114659.0	112826.0	GSM2776971 r2	0:75.92 1:75.77	A:3541924;C:4724849;G:5837104;T:3008086;N:2696	75	75	3541924	4724849	5837104	3008086	2696	SRX3171476	SRS2501286	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00319	0.00885	0.00255	0.00577	0.99924	0.99685	0.35849	0.57471	76	74	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43554	43554	SRR6020372	SRX3171475	SRS2501283	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Trans	GSM2776970	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776970	GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq	GSM2776970	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-eye_Trans_p01_R1.fastq.gz R3_right-eye_Trans_p01_R2.fastq.gz	fastq fastq	1232363344.0	8159367.0	GSM2776970 r1	0:75.57 1:75.47	A:358721828;C:215851348;G:306533357;T:351024145;N:232666	75	75	358721828	215851348	306533357	351024145	232666	SRX3171475	SRS2501283	SRA602108	GEO	AVO, Hubrecht Institue	2	0.03878	0.48751	0.02989	0.31199	0.9932	0.95678	0.49115	0.57852	75	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43555	43555	SRR6020373	SRX3171475	SRS2501283	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Trans	GSM2776970	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776970	GSM2776970: R3 right eye Trans; Danio rerio; RNA Seq	GSM2776970	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-eye_Trans_p02_R1.fastq.gz R3_right-eye_Trans_p02_R2.fastq.gz	fastq fastq	13506918357.0	89381621.0	GSM2776970 r2	0:75.55 1:75.57	A:4378616211;C:1844732259;G:3577317917;T:3703682555;N:2569415	75	75	4378616211	1844732259	3577317917	3703682555	2569415	SRX3171475	SRS2501283	SRA602108	GEO	AVO, Hubrecht Institue	2	0.13968	0.38495	0.10884	0.24752	0.99393	0.97179	0.42155	0.58172	76	75	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43556	43556	SRR6020370	SRX3171474	SRS2501284	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Scar	GSM2776969	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776969	GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq	GSM2776969	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776969	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-eye_Scar_p01_R1.fastq.gz R3_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	16402556.0	107973.0	GSM2776969 r1	0:75.98 1:75.94	A:2913035;C:4716394;G:6012715;T:2757706;N:2706	75	75	2913035	4716394	6012715	2757706	2706	SRX3171474	SRS2501284	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00031	0.00215	0.00027	0.00065	0.99995	0.99941	0.5	0.375	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43557	43557	SRR6020371	SRX3171474	SRS2501284	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 right eye Scar	GSM2776969	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	R3 right eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	right eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:right eye\|sorted plates:2	GSM2776969	GSM2776969: R3 right eye Scar; Danio rerio; RNA Seq	GSM2776969	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776969	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_right-eye_Scar_p02_R1.fastq.gz R3_right-eye_Scar_p02_R2.fastq.gz	fastq fastq	9167189.0	60361.0	GSM2776969 r2	0:75.94 1:75.94	A:1738353;C:2524474;G:3359567;T:1542690;N:2105	75	75	1738353	2524474	3359567	1542690	2105	SRX3171474	SRS2501284	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00212	0.01274	0.00127	0.00362	0.99955	0.99815	0.27586	0.42201	76	75	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43558	43558	SRR6020369	SRX3171473	SRS2501282	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 left eye Scar	GSM2776968	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:left eye\|sorted plates:1	R3 left eye Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	left eye single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:left eye\|sorted plates:1	GSM2776968	GSM2776968: R3 left eye Scar; Danio rerio; RNA Seq	GSM2776968	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776968	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_left-eye_Scar_p01_R1.fastq.gz R3_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	3260057.0	21462.0	GSM2776968 r1	0:75.94 1:75.96	A:576368;C:943970;G:1229076;T:510377;N:266	75	75	576368	943970	1229076	510377	266	SRX3171473	SRS2501282	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00061	0.00925	0.0003	0.00287	0.99991	0.99947	0.5	0.62962	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43559	43559	SRR6020367	SRX3171472	SRS2501281	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 hindbrain Scar	GSM2776967	source name:hindbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:hindbrain\|sorted plates:2	R3 hindbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	hindbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:hindbrain\|sorted plates:2	GSM2776967	GSM2776967: R3 hindbrain Scar; Danio rerio; RNA Seq	GSM2776967	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776967	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_hindbrain_Scar_p01_R1.fastq.gz R3_hindbrain_Scar_p01_R2.fastq.gz	fastq fastq	115690866.0	761578.0	GSM2776967 r1	0:75.98 1:75.93	A:20512701;C:33555342;G:43229736;T:18385623;N:7464	75	75	20512701	33555342	43229736	18385623	7464	SRX3171472	SRS2501281	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00193	0.00517	0.00169	0.00424	0.99926	0.99707	0.48837	0.46875	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43560	43560	SRR6020368	SRX3171472	SRS2501281	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 hindbrain Scar	GSM2776967	source name:hindbrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:hindbrain\|sorted plates:2	R3 hindbrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	hindbrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:hindbrain\|sorted plates:2	GSM2776967	GSM2776967: R3 hindbrain Scar; Danio rerio; RNA Seq	GSM2776967	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776967	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_hindbrain_Scar_p02_R1.fastq.gz R3_hindbrain_Scar_p02_R2.fastq.gz	fastq fastq	208002759.0	1369368.0	GSM2776967 r2	0:75.98 1:75.92	A:37856903;C:60123242;G:77023348;T:32985516;N:13750	75	75	37856903	60123242	77023348	32985516	13750	SRX3171472	SRS2501281	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00064	0.00019	0.0005	0.00013	0.99989	0.99989	0.0	0.25	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43561	43561	SRR6020365	SRX3171471	SRS2501280	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 forebrain Trans	GSM2776966	source name:forebrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	R3 forebrain Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	forebrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	GSM2776966	GSM2776966: R3 forebrain Trans; Danio rerio; RNA Seq	GSM2776966	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776966	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_forebrain_Trans_p01_R1.fastq.gz R3_forebrain_Trans_p01_R2.fastq.gz	fastq fastq	18386653889.0	121934623.0	GSM2776966 r1	0:75.36 1:75.44	A:5368597664;C:3836072358;G:4591907490;T:4589768111;N:308266	75	75	5368597664	3836072358	4591907490	4589768111	308266	SRX3171471	SRS2501280	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00673	0.01503	0.00454	0.01051	0.99691	0.99496	0.61921	0.70967	74	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43562	43562	SRR6020366	SRX3171471	SRS2501280	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 forebrain Trans	GSM2776966	source name:forebrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	R3 forebrain Trans	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	forebrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	GSM2776966	GSM2776966: R3 forebrain Trans; Danio rerio; RNA Seq	GSM2776966	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776966	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_forebrain_Trans_p02_R1.fastq.gz R3_forebrain_Trans_p02_R2.fastq.gz	fastq fastq	21437781385.0	142145763.0	GSM2776966 r2	0:75.37 1:75.44	A:6314729991;C:4205041207;G:5479780347;T:5437855057;N:374783	75	75	6314729991	4205041207	5479780347	5437855057	374783	SRX3171471	SRS2501280	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00949	0.01651	0.0072	0.01315	0.99722	0.99504	0.56842	0.59162	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43563	43563	SRR6020363	SRX3171470	SRS2501279	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 forebrain Scar	GSM2776965	source name:forebrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	R3 forebrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	forebrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	GSM2776965	GSM2776965: R3 forebrain Scar; Danio rerio; RNA Seq	GSM2776965	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776965	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_forebrain_Scar_p01_R1.fastq.gz R3_forebrain_Scar_p01_R2.fastq.gz	fastq fastq	1193678975.0	7860693.0	GSM2776965 r1	0:75.98 1:75.88	A:210134147;C:347073995;G:448865724;T:187527052;N:78057	75	75	210134147	347073995	448865724	187527052	78057	SRX3171470	SRS2501279	SRA602108	GEO	AVO, Hubrecht Institue	2	2e-05	4e-05	1e-05	2e-05	1.0	0.99995		0.5	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System
43564	43564	SRR6020364	SRX3171470	SRS2501279	SRP116018	PRJNA399711	Whole organism clone tracing using single cell sequencing	GSE102990	Transcriptome Analysis	We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.	pubmed:29590089	R3 forebrain Scar	GSM2776965	source name:forebrain single cells\|cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	R3 forebrain Scar	In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the transcriptome.txt.gz files.	forebrain single cells	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	cas9 injection:mRNA\|FISH id:R3\|tissue:forebrain\|sorted plates:2	GSM2776965	GSM2776965: R3 forebrain Scar; Danio rerio; RNA Seq	GSM2776965	1	post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters	GEO Accession:GSM2776965	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R3_forebrain_Scar_p02_R1.fastq.gz R3_forebrain_Scar_p02_R2.fastq.gz	fastq fastq	470834444.0	3100292.0	GSM2776965 r2	0:75.97 1:75.90	A:83238909;C:136679646;G:176795270;T:74088151;N:32468	75	75	83238909	136679646	176795270	74088151	32468	SRX3171470	SRS2501279	SRA602108	GEO	AVO, Hubrecht Institue	2	1e-05	3e-05	0.0	1e-05	0.99997	0.99995	0.0	0.33333	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-09-08	Undetermined	Multi-stage	Brain	Nervous System

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