metadata: run_metadata: 16 rows where experiment.platform = "ILLUMINA", technology = "scartrace" and tissue_curation

16 rows where experiment.platform = "ILLUMINA", technology = "scartrace" and tissue_curation_coarse = "Sensory System"

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
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
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
43605	43605	SRR6020322	SRX3171463	SRS2501272	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	R1 right eye Trans	GSM2776958	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	R1 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:R1\|tissue:right eye\|sorted plates:1	GSM2776958	GSM2776958: R1 right eye Trans; Danio rerio; RNA Seq	GSM2776958	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:GSM2776958	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_right-eye_Trans_p01_R1.fastq.gz R1_right-eye_Trans_p01_R2.fastq.gz	fastq fastq	5130322003.0	34025983.0	GSM2776958 r1	0:75.43 1:75.35	A:1849671847;C:731930699;G:648670890;T:1898907330;N:1141237	75	75	1849671847	731930699	648670890	1898907330	1141237	SRX3171463	SRS2501272	SRA602108	GEO	AVO, Hubrecht Institue	2	0.2345	0.49487	0.17483	0.32246	0.9683	0.91938	0.50419	0.54579	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
43606	43606	SRR6020321	SRX3171462	SRS2501271	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	R1 right eye Scar	GSM2776957	source name:right eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:right eye\|sorted plates:1	R1 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:R1\|tissue:right eye\|sorted plates:1	GSM2776957	GSM2776957: R1 right eye Scar; Danio rerio; RNA Seq	GSM2776957	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:GSM2776957	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_right-eye_Scar_p01_R1.fastq.gz R1_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	51349725.0	338093.0	GSM2776957 r1	0:75.98 1:75.90	A:9493047;C:14848060;G:18750237;T:8248478;N:9903	75	75	9493047	14848060	18750237	8248478	9903	SRX3171462	SRS2501271	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	0.00029	0.00011	0.00021	0.99993	0.99985	0.66666	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	Eye	Sensory System
43611	43611	SRR6020315	SRX3171459	SRS2501268	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	R1 left eye Trans	GSM2776954	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left 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.	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:R1\|tissue:left eye\|sorted plates:2	GSM2776954	GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq	GSM2776954	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:GSM2776954	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_left-eye_Trans_p01_R1.fastq.gz R1_left-eye_Trans_p01_R2.fastq.gz	fastq fastq	1046170155.0	6918434.0	GSM2776954 r1	0:75.69 1:75.52	A:295576695;C:221931427;G:229805854;T:298632621;N:223558	75	75	295576695	221931427	229805854	298632621	223558	SRX3171459	SRS2501268	SRA602108	GEO	AVO, Hubrecht Institue	2	0.06872	0.17373	0.05659	0.12922	0.9833	0.95611	0.46872	0.54838	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	Eye	Sensory System
43612	43612	SRR6020316	SRX3171459	SRS2501268	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	R1 left eye Trans	GSM2776954	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 left 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.	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:R1\|tissue:left eye\|sorted plates:2	GSM2776954	GSM2776954: R1 left eye Trans; Danio rerio; RNA Seq	GSM2776954	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:GSM2776954	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_left-eye_Trans_p02_R2.fastq.gz R1_left-eye_Trans_p02_R1.fastq.gz	fastq fastq	25047483725.0	165912644.0	GSM2776954 r2	0:75.59 1:75.38	A:6912192763;C:5496852975;G:6032128490;T:6600903816;N:5405681	75	75	6912192763	5496852975	6032128490	6600903816	5405681	SRX3171459	SRS2501268	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01804	0.04542	0.01535	0.03794	0.99492	0.98774	0.42283	0.45955	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
43613	43613	SRR6020313	SRX3171458	SRS2501266	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	R1 left eye Scar	GSM2776953	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 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:R1\|tissue:left eye\|sorted plates:2	GSM2776953	GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq	GSM2776953	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:GSM2776953	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_left-eye_Scar_p01_R1.fastq.gz R1_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	430346860.0	2834154.0	GSM2776953 r1	0:75.96 1:75.88	A:78839865;C:124580997;G:157976167;T:68821337;N:128494	75	75	78839865	124580997	157976167	68821337	128494	SRX3171458	SRS2501266	SRA602108	GEO	AVO, Hubrecht Institue	2	9e-05	1e-05	5e-05	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	2017-09-08	Undetermined	Multi-stage	Eye	Sensory System
43614	43614	SRR6020314	SRX3171458	SRS2501266	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	R1 left eye Scar	GSM2776953	source name:left eye single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:left eye\|sorted plates:2	R1 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:R1\|tissue:left eye\|sorted plates:2	GSM2776953	GSM2776953: R1 left eye Scar; Danio rerio; RNA Seq	GSM2776953	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:GSM2776953	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_left-eye_Scar_p02_R1.fastq.gz R1_left-eye_Scar_p02_R2.fastq.gz	fastq fastq	840951649.0	5536337.0	GSM2776953 r2	0:75.98 1:75.91	A:151508446;C:241728170;G:312991163;T:134635263;N:88607	75	75	151508446	241728170	312991163	134635263	88607	SRX3171458	SRS2501266	SRA602108	GEO	AVO, Hubrecht Institue	2	8e-05	3e-05	5e-05	0.0	0.99997	0.99993	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	Eye	Sensory System
43626	43626	SRR5961764	SRX3119875	SRS2454734	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 right eye Scars	GSM2752198	source name:right eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	P1 right eye Scars	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 and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence 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	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:P1\|tissue:right eye\|sorted plates:2	GSM2752198	GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq	GSM2752198	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:GSM2752198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P1_right-eye_Scar_p01_R1.fastq.gz P1_right-eye_Scar_p01_R2.fastq.gz	fastq fastq	41294204.0	271740.0	GSM2752198 r1	0:75.99 1:75.97	A:7444211;C:11950093;G:15212116;T:6685156;N:2628	75	75	7444211	11950093	15212116	6685156	2628	SRX3119875	SRS2454734	SRA602108	GEO	AVO, Hubrecht Institue	2	6e-05	0.00023	4e-05	0.00017	0.99993	0.99981	0.66666	0.66666	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-08-23	Undetermined	Multi-stage	Eye	Sensory System
43627	43627	SRR6930577	SRX3119875	SRS2454734	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 right eye Scars	GSM2752198	source name:right eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:right eye\|sorted plates:2	P1 right eye Scars	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 and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence 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	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:P1\|tissue:right eye\|sorted plates:2	GSM2752198	GSM2752198: P1 right eye Scars; Danio rerio; RNA Seq	GSM2752198	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:GSM2752198	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P1_right-eye_Scar_p02_R1.fastq.gz P1_right-eye_Scar_p02_R2.fastq.gz	fastq fastq	91033438.0	599208.0	GSM2752198 r2	0:75.97 1:75.96	A:16805120;C:25814395;G:33115601;T:15269609;N:28713	75	75	16805120	25814395	33115601	15269609	28713	SRX3119875	SRS2454734	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00381	0.00672	0.00333	0.00593	0.99845	0.9975	0.45238	0.50769	76	76	T	T	mates < 9% mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	other_seq	scartrace	Netherlands	2017-08-23	Undetermined	Multi-stage	Eye	Sensory System
43629	43629	SRR5961762	SRX3119873	SRS2454732	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 left eye Scars	GSM2752196	source name:left eye single cells\|cas9 injection:protein\|FISH id:P1\|tissue:left eye\|sorted plates:1	P1 left eye Scars	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 and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence 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	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:P1\|tissue:left eye\|sorted plates:1	GSM2752196	GSM2752196: P1 left eye Scars; Danio rerio; RNA Seq	GSM2752196	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:GSM2752196	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P1_left-eye_Scar_p01_R1.fastq.gz P1_left-eye_Scar_p01_R2.fastq.gz	fastq fastq	161576029.0	1063213.0	GSM2752196 r1	0:75.98 1:75.99	A:29049869;C:46414226;G:59509149;T:26592886;N:9899	75	75	29049869	46414226	59509149	26592886	9899	SRX3119873	SRS2454732	SRA602108	GEO	AVO, Hubrecht Institue	2	1e-05	2e-05	0.0	0.0	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	2017-08-23	Undetermined	Multi-stage	Eye	Sensory 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");;