metadata: run_metadata: 48 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "scartrace" and tissue_curation

48 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "scartrace" and tissue_curation_coarse = "Renal 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
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
43565	43565	SRR6020354	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p01_R2.fastq.gz R2_wkm_Trans_p01_R1.fastq.gz	fastq fastq	9024550362.0	59819416.0	GSM2776964 r1	0:75.43 1:75.43	A:2680475382;C:1320224241;G:1470728320;T:3553005800;N:116619	75	75	2680475382	1320224241	1470728320	3553005800	116619	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.3361	0.6658	0.26022	0.30025	0.9655	0.84861	0.54877	0.53502	73	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
43566	43566	SRR6020355	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p02_R1.fastq.gz R2_wkm_Trans_p02_R2.fastq.gz	fastq fastq	6846456986.0	45296050.0	GSM2776964 r2	0:75.58 1:75.57	A:1794290868;C:1266097894;G:1480877558;T:2305103809;N:86857	75	75	1794290868	1266097894	1480877558	2305103809	86857	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.12369	0.58191	0.08122	0.21507	0.96917	0.86478	0.54436	0.52833	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
43567	43567	SRR6020356	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p04_R1.fastq.gz R2_wkm_Trans_p04_R2.fastq.gz	fastq fastq	6833024281.0	45038138.0	GSM2776964 r3	0:75.92 1:75.80	A:1377999605;C:1844050318;G:2309866401;T:1300399227;N:708730	75	75	1377999605	1844050318	2309866401	1300399227	708730	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01228	0.03967	0.01047	0.02854	0.996	0.98784	0.46886	0.40014	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
43568	43568	SRR6020357	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p05_R1.fastq.gz R2_wkm_Trans_p05_R2.fastq.gz	fastq fastq	10064318519.0	66330889.0	GSM2776964 r4	0:75.93 1:75.80	A:2012776438;C:2737247628;G:3409080553;T:1904157367;N:1056533	75	75	2012776438	2737247628	3409080553	1904157367	1056533	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01861	0.04126	0.01632	0.03024	0.99537	0.9852	0.46531	0.52808	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
43569	43569	SRR6020358	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p06_R1.fastq.gz R2_wkm_Trans_p06_R2.fastq.gz	fastq fastq	6687331360.0	44108617.0	GSM2776964 r5	0:75.86 1:75.75	A:1437098890;C:1744557843;G:2166182975;T:1338781574;N:710078	75	75	1437098890	1744557843	2166182975	1338781574	710078	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.02427	0.05957	0.02134	0.04215	0.99504	0.98561	0.59024	0.56702	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
43570	43570	SRR6020359	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p07_R1.fastq.gz R2_wkm_Trans_p07_R2.fastq.gz	fastq fastq	5153832004.0	34073366.0	GSM2776964 r6	0:75.66 1:75.60	A:1326888770;C:1102939496;G:1274553839;T:1448364985;N:1084914	75	75	1326888770	1102939496	1274553839	1448364985	1084914	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.1589	0.37012	0.13594	0.2937	0.96008	0.89796	0.53952	0.50866	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	Kidney	Renal System
43571	43571	SRR6020360	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p08_R1.fastq.gz R2_wkm_Trans_p08_R2.fastq.gz	fastq fastq	6115949904.0	40453679.0	GSM2776964 r7	0:75.63 1:75.55	A:1597313172;C:1289666072;G:1493416158;T:1734258580;N:1295922	75	75	1597313172	1289666072	1493416158	1734258580	1295922	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.13807	0.341	0.11368	0.25445	0.96546	0.90859	0.52718	0.49692	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
43572	43572	SRR6020361	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p09_R1.fastq.gz R2_wkm_Trans_p09_R2.fastq.gz	fastq fastq	5237730043.0	34642054.0	GSM2776964 r8	0:75.63 1:75.57	A:1366106800;C:1100303416;G:1291870046;T:1478328279;N:1121502	75	75	1366106800	1100303416	1291870046	1478328279	1121502	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.12743	0.30857	0.10066	0.19993	0.96899	0.91999	0.50164	0.55176	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
43573	43573	SRR6020362	SRX3171469	SRS2501278	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	R2 wkm Trans	GSM2776964	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776964	GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq	GSM2776964	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:GSM2776964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Trans_p10_R2.fastq.gz R2_wkm_Trans_p10_R1.fastq.gz	fastq fastq	5966158980.0	39481315.0	GSM2776964 r9	0:75.59 1:75.53	A:1608448002;C:1182029002;G:1349064196;T:1825357615;N:1260165	75	75	1608448002	1182029002	1349064196	1825357615	1260165	SRX3171469	SRS2501278	SRA602108	GEO	AVO, Hubrecht Institue	2	0.14278	0.40505	0.11298	0.25782	0.96169	0.88933	0.53335	0.51935	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	Kidney	Renal System
43574	43574	SRR6020345	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p01_R1.fastq.gz R2_wkm_Scar_p01_R2.fastq.gz	fastq fastq	1684853042.0	11092789.0	GSM2776963 r1	0:75.97 1:75.92	A:295001511;C:489169550;G:629447507;T:271215194;N:19280	75	75	295001511	489169550	629447507	271215194	19280	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00026	0.00111	0.00021	0.00081	0.99983	0.99931	0.625	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	Kidney	Renal System
43575	43575	SRR6020346	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p02_R1.fastq.gz R2_wkm_Scar_p02_R2.fastq.gz	fastq fastq	2167767595.0	14269042.0	GSM2776963 r2	0:75.97 1:75.95	A:393119574;C:622441995;G:803855479;T:348326899;N:23648	75	75	393119574	622441995	803855479	348326899	23648	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	4e-05	0.00012	2e-05	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	Kidney	Renal System
43576	43576	SRR6020347	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p04_R1.fastq.gz R2_wkm_Scar_p04_R2.fastq.gz	fastq fastq	949039352.0	6246899.0	GSM2776963 r3	0:75.98 1:75.94	A:168664399;C:275210713;G:354697026;T:150353667;N:113547	75	75	168664399	275210713	354697026	150353667	113547	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	5e-05	1e-05	4e-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	Kidney	Renal System
43577	43577	SRR6020348	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p05_R1.fastq.gz R2_wkm_Scar_p05_R2.fastq.gz	fastq fastq	708086378.0	4660800.0	GSM2776963 r4	0:75.98 1:75.94	A:125487931;C:204868898;G:265817122;T:111841010;N:71417	75	75	125487931	204868898	265817122	111841010	71417	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	5e-05	0.0	3e-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	Kidney	Renal System
43578	43578	SRR6020349	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p06_R1.fastq.gz R2_wkm_Scar_p06_R2.fastq.gz	fastq fastq	1334977556.0	8786739.0	GSM2776963 r5	0:75.98 1:75.95	A:236705935;C:386768904;G:500728970;T:210637790;N:135957	75	75	236705935	386768904	500728970	210637790	135957	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	2e-05	0.0	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	Kidney	Renal System
43579	43579	SRR6020350	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p07_R1.fastq.gz R2_wkm_Scar_p07_R2.fastq.gz	fastq fastq	560151517.0	3686527.0	GSM2776963 r6	0:75.99 1:75.96	A:99216542;C:162559282;G:209970335;T:88295033;N:110325	75	75	99216542	162559282	209970335	88295033	110325	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00013	0.00031	0.0001	0.00024	0.99989	0.99977	0.4	0.18181	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
43580	43580	SRR6020351	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p08_R1.fastq.gz R2_wkm_Scar_p08_R2.fastq.gz	fastq fastq	581077562.0	3824465.0	GSM2776963 r7	0:75.98 1:75.95	A:103035022;C:167783256;G:218182356;T:91955266;N:121662	75	75	103035022	167783256	218182356	91955266	121662	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00012	0.00017	0.0001	0.0001	0.99995	0.99983	0.33333	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
43581	43581	SRR6020352	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p09_R1.fastq.gz R2_wkm_Scar_p09_R2.fastq.gz	fastq fastq	540845179.0	3559589.0	GSM2776963 r8	0:75.98 1:75.96	A:95821696;C:156515054;G:202433894;T:85962271;N:112264	75	75	95821696	156515054	202433894	85962271	112264	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00022	0.00026	0.00017	0.00017	0.99985	0.99975	0.42857	0.61538	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
43582	43582	SRR6020353	SRX3171468	SRS2501277	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	R2 wkm Scar	GSM2776963	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R2\|tissue:whole kidney marrow\|sorted plates:9	R2 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:R2\|tissue:whole kidney marrow\|sorted plates:9	GSM2776963	GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq	GSM2776963	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:GSM2776963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R2_wkm_Scar_p10_R1.fastq.gz R2_wkm_Scar_p10_R2.fastq.gz	fastq fastq	839350049.0	5524195.0	GSM2776963 r9	0:75.98 1:75.96	A:148919223;C:243407956;G:314166938;T:132682976;N:172956	75	75	148919223	243407956	314166938	132682976	172956	SRX3171468	SRS2501277	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00026	0.00065	0.00022	0.00044	0.99987	0.99935	0.5	0.69696	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
43583	43583	SRR6020335	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p01_R1.fastq.gz R1_wkm_Trans_p01_R2.fastq.gz	fastq fastq	5973924896.0	39414942.0	GSM2776962 r1	0:75.90 1:75.67	A:1246713886;C:1600299713;G:1930846373;T:1194812009;N:1252915	75	75	1246713886	1600299713	1930846373	1194812009	1252915	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01167	0.032	0.00909	0.02214	0.99644	0.98829	0.31168	0.44038	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
43584	43584	SRR6020336	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p10_R1.fastq.gz R1_wkm_Trans_p10_R2.fastq.gz	fastq fastq	2617289615.0	17271557.0	GSM2776962 r10	0:75.82 1:75.72	A:567948720;C:650310169;G:793147028;T:605454241;N:429457	75	75	567948720	650310169	793147028	605454241	429457	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.0644	0.15708	0.05669	0.13057	0.98198	0.94714	0.50177	0.51068	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	Kidney	Renal System
43585	43585	SRR6020337	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p02_R1.fastq.gz R1_wkm_Trans_p02_R2.fastq.gz	fastq fastq	7594280551.0	50128244.0	GSM2776962 r2	0:75.86 1:75.63	A:1634649789;C:1975593425;G:2355482941;T:1626855827;N:1698569	75	75	1634649789	1975593425	2355482941	1626855827	1698569	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01418	0.05132	0.01052	0.03283	0.99411	0.98096	0.42315	0.47699	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
43586	43586	SRR6020338	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p03_R1.fastq.gz R1_wkm_Trans_p03_R2.fastq.gz	fastq fastq	10033302083.0	66227671.0	GSM2776962 r3	0:75.87 1:75.63	A:2174708635;C:2640912986;G:3104545578;T:2110890445;N:2244439	75	75	2174708635	2640912986	3104545578	2110890445	2244439	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01909	0.05761	0.01497	0.0388	0.99527	0.98559	0.62157	0.383	75	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
43587	43587	SRR6020339	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p04_R1.fastq.gz R1_wkm_Trans_p04_R2.fastq.gz	fastq fastq	6711074817.0	44294742.0	GSM2776962 r4	0:75.86 1:75.65	A:1427276784;C:1758105877;G:2110503657;T:1413707482;N:1481017	75	75	1427276784	1758105877	2110503657	1413707482	1481017	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01603	0.04728	0.01155	0.02826	0.99537	0.98275	0.40869	0.46908	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
43588	43588	SRR6020340	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p05_R1.fastq.gz R1_wkm_Trans_p05_R2.fastq.gz	fastq fastq	5218937446.0	34471555.0	GSM2776962 r5	0:75.81 1:75.59	A:1215811466;C:1256980753;G:1501056299;T:1243910449;N:1178479	75	75	1215811466	1256980753	1501056299	1243910449	1178479	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.02337	0.08686	0.0188	0.05946	0.99561	0.98139	0.29979	0.497	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
43589	43589	SRR6020341	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p06_R1.fastq.gz R1_wkm_Trans_p06_R2.fastq.gz	fastq fastq	6108807000.0	40436337.0	GSM2776962 r6	0:75.61 1:75.47	A:1673719828;C:1137235460;G:1275308369;T:2021133061;N:1410282	75	75	1673719828	1137235460	1275308369	2021133061	1410282	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.10437	0.31204	0.0749	0.16508	0.97881	0.92991	0.45043	0.51006	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	Kidney	Renal System
43590	43590	SRR6020342	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p07_R1.fastq.gz R1_wkm_Trans_p07_R2.fastq.gz	fastq fastq	4731732871.0	31235538.0	GSM2776962 r7	0:75.80 1:75.69	A:1076749811;C:1116149409;G:1331817067;T:1206252219;N:764365	75	75	1076749811	1116149409	1331817067	1206252219	764365	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.06387	0.1773	0.05441	0.13368	0.98293	0.93825	0.51607	0.52472	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	Kidney	Renal System
43591	43591	SRR6020343	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p08_R1.fastq.gz R1_wkm_Trans_p08_R2.fastq.gz	fastq fastq	4880262283.0	32178172.0	GSM2776962 r8	0:75.90 1:75.76	A:984048995;C:1311633495;G:1623325534;T:960451784;N:802475	75	75	984048995	1311633495	1623325534	960451784	802475	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.01625	0.04758	0.01254	0.03334	0.99119	0.97512	0.51741	0.48393	75	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
43592	43592	SRR6020344	SRX3171467	SRS2501276	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 wkm Trans	GSM2776962	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776962	GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq	GSM2776962	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:GSM2776962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Trans_p09_R1.fastq.gz R1_wkm_Trans_p09_R2.fastq.gz	fastq fastq	2281506515.0	15040814.0	GSM2776962 r9	0:75.91 1:75.78	A:455027935;C:614063661;G:762091600;T:449957278;N:366041	75	75	455027935	614063661	762091600	449957278	366041	SRX3171467	SRS2501276	SRA602108	GEO	AVO, Hubrecht Institue	2	0.02501	0.0603	0.022	0.04691	0.99159	0.97228	0.50712	0.52872	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
43593	43593	SRR6020325	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p01_R1.fastq.gz R1_wkm_Scar_p01_R2.fastq.gz	fastq fastq	1160781646.0	7644126.0	GSM2776961 r1	0:75.98 1:75.87	A:206133465;C:337727978;G:433057561;T:183619190;N:243452	75	75	206133465	337727978	433057561	183619190	243452	SRX3171466	SRS2501275	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	Kidney	Renal System
43594	43594	SRR6020326	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p10_R1.fastq.gz R1_wkm_Scar_p10_R2.fastq.gz	fastq fastq	444321370.0	2925523.0	GSM2776961 r10	0:75.98 1:75.89	A:78895877;C:128614562;G:165020269;T:71718452;N:72210	75	75	78895877	128614562	165020269	71718452	72210	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00013	0.00022	8e-05	0.0001	0.99995	0.99969	0.0	0.4375	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
43595	43595	SRR6020327	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p02_R1.fastq.gz R1_wkm_Scar_p02_R2.fastq.gz	fastq fastq	1118531897.0	7366750.0	GSM2776961 r2	0:75.98 1:75.85	A:199272195;C:323746349;G:416605188;T:178669664;N:238501	75	75	199272195	323746349	416605188	178669664	238501	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	2e-05	9e-05	0.0	2e-05	0.99997	0.99987	1.0	0.28571	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
43596	43596	SRR6020328	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p03_R1.fastq.gz R1_wkm_Scar_p03_R2.fastq.gz	fastq fastq	842900122.0	5552138.0	GSM2776961 r3	0:75.98 1:75.83	A:149698513;C:244376973;G:313988330;T:134655045;N:181261	75	75	149698513	244376973	313988330	134655045	181261	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	5e-05	9e-05	2e-05	4e-05	0.99993	0.99989	0.66666	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	Kidney	Renal System
43597	43597	SRR6020329	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p04_R1.fastq.gz R1_wkm_Scar_p04_R2.fastq.gz	fastq fastq	983580857.0	6477811.0	GSM2776961 r4	0:75.98 1:75.86	A:173458414;C:285222602;G:367968109;T:156722927;N:208805	75	75	173458414	285222602	367968109	156722927	208805	SRX3171466	SRS2501275	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	Kidney	Renal System
43598	43598	SRR6020330	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p05_R1.fastq.gz R1_wkm_Scar_p05_R2.fastq.gz	fastq fastq	542048001.0	3570304.0	GSM2776961 r5	0:75.98 1:75.84	A:96887298;C:156549850;G:201875058;T:86619073;N:116722	75	75	96887298	156549850	201875058	86619073	116722	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	5e-05	1e-05	3e-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	Kidney	Renal System
43599	43599	SRR6020331	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p06_R1.fastq.gz R1_wkm_Scar_p06_R2.fastq.gz	fastq fastq	1331503316.0	8770302.0	GSM2776961 r6	0:75.98 1:75.84	A:239821115;C:383865311;G:491153102;T:216395981;N:267807	75	75	239821115	383865311	491153102	216395981	267807	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00035	0.00029	0.00023	0.00015	0.99989	0.99973	0.125	0.46153	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
43600	43600	SRR6020332	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p07_R1.fastq.gz R1_wkm_Scar_p07_R2.fastq.gz	fastq fastq	443058723.0	2917225.0	GSM2776961 r7	0:75.99 1:75.89	A:78132383;C:128408112;G:164997328;T:71447465;N:73435	75	75	78132383	128408112	164997328	71447465	73435	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00011	0.00017	8e-05	0.00014	0.99993	0.99991	0.25	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	Kidney	Renal System
43601	43601	SRR6020333	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p08_R1.fastq.gz R1_wkm_Scar_p08_R2.fastq.gz	fastq fastq	460136778.0	3029705.0	GSM2776961 r8	0:75.99 1:75.89	A:81219078;C:133929839;G:170892657;T:74024644;N:70560	75	75	81219078	133929839	170892657	74024644	70560	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	2e-05	2e-05	1e-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	Kidney	Renal System
43602	43602	SRR6020334	SRX3171466	SRS2501275	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 wkm Scar	GSM2776961	source name:wkm single cells\|cas9 injection:mRNA\|FISH id:R1\|tissue:whole kidney marrow\|sorted plates:10	R1 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:R1\|tissue:whole kidney marrow\|sorted plates:10	GSM2776961	GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq	GSM2776961	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:GSM2776961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	R1_wkm_Scar_p09_R1.fastq.gz R1_wkm_Scar_p09_R2.fastq.gz	fastq fastq	495182451.0	3261129.0	GSM2776961 r9	0:75.98 1:75.87	A:89479589;C:142929535;G:181791653;T:80902228;N:79446	75	75	89479589	142929535	181791653	80902228	79446	SRX3171466	SRS2501275	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00037	0.00149	0.00026	0.00096	0.99969	0.99855	0.22222	0.3647	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
43634	43634	SRR5961758	SRX3119870	SRS2454729	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 wkm Scars	GSM2752193	source name:wkm single cells\|cas9 injection:protein\|FISH id:P1\|tissue:whole kidney marrow\|sorted plates:2	P1 wkm 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	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:P1\|tissue:whole kidney marrow\|sorted plates:2	GSM2752193	GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq	GSM2752193	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:GSM2752193	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P1_wkm_Scar_p01_R1.fastq.gz P1_wkm_Scar_p01_R2.fastq.gz	fastq fastq	995569951.0	6550623.0	GSM2752193 r1	0:75.99 1:75.99	A:179447412;C:292592664;G:370193004;T:153293464;N:43407	75	75	179447412	292592664	370193004	153293464	43407	SRX3119870	SRS2454729	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00015	4e-05	0.00013	3e-05	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	2017-08-23	Undetermined	Multi-stage	Kidney	Renal System
43635	43635	SRR5961759	SRX3119870	SRS2454729	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 wkm Scars	GSM2752193	source name:wkm single cells\|cas9 injection:protein\|FISH id:P1\|tissue:whole kidney marrow\|sorted plates:2	P1 wkm 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	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:P1\|tissue:whole kidney marrow\|sorted plates:2	GSM2752193	GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq	GSM2752193	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:GSM2752193	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP116018	P1_wkm_Scar_p02_R1.fastq.gz P1_wkm_Scar_p02_R2.fastq.gz	fastq fastq	941664617.0	6196187.0	GSM2752193 r2	0:75.99 1:75.99	A:170094338;C:275555653;G:348702043;T:147269855;N:42728	75	75	170094338	275555653	348702043	147269855	42728	SRX3119870	SRS2454729	SRA602108	GEO	AVO, Hubrecht Institue	2	0.00033	0.0001	0.00027	8e-05	0.99987	0.99993	0.625	1.0	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	Kidney	Renal 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");;