{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"scartrace\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[43472, "SRR6888831", "SRX3839382", "SRS3086668", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "P2 cfin vent Scar", "GSM3065988", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P2 cfin vent Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065988", "GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq", "GSM3065988", null, "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. 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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.", null, "pubmed:29590089", null, "P2 cfin vent Scar", "GSM3065988", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P2 cfin vent Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065988", "GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq", "GSM3065988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz", "fastq fastq", 110701966.0, 728490.0, "GSM3065988 r2", "0:75.99 1:75.97", "A:19507928;C:32552811;G:40930271;T:17699467;N:11489", 75, 75, null, null, 19507928, 32552811, 40930271, 17699467, 11489, "SRX3839382", "SRS3086668", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00021, 0.0004, 0.00015, 0.00031, 0.99991, 0.99981, 1.0, 0.84615, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43474, "SRR6888829", "SRX3839381", "SRS3086670", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "P1 cfin dorsal Scar", "GSM3065987", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P1 cfin dorsal Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065987", "GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq", "GSM3065987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Dors-003-Scar_R2.fastq.gz P2-CFin-Dors-003-Scar_R1.fastq.gz", "fastq fastq", 537943644.0, 3539989.0, "GSM3065987 r1", "0:75.99 1:75.97", "A:94708808;C:157878001;G:198461680;T:86838061;N:57094", 75, 75, null, null, 94708808, 157878001, 198461680, 86838061, 57094, "SRX3839381", "SRS3086670", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00016, 0.00102, 0.0001, 0.00067, 0.99995, 0.99995, 0.0, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43475, "SRR6888830", "SRX3839381", "SRS3086670", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "P1 cfin dorsal Scar", "GSM3065987", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P1 cfin dorsal Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065987", "GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq", "GSM3065987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz", "fastq fastq", 856597590.0, 5637115.0, "GSM3065987 r2", "0:75.99 1:75.97", "A:151359975;C:251587454;G:317011744;T:136549208;N:89209", 75, 75, null, null, 151359975, 251587454, 317011744, 136549208, 89209, "SRX3839381", "SRS3086670", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00027, 0.00065, 0.00016, 0.00039, 0.99975, 0.99951, 0.29411, 0.53658, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43476, "SRR6020446", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p01_R1.fastq.gz R5_sec_Trans_p01_R2.fastq.gz", "fastq fastq", 5031589058.0, 33202740.0, "GSM2776988 r1", "0:75.79 1:75.75", "A:1144328847;C:1211156155;G:1480041764;T:1195826451;N:235841", 75, 75, null, null, 1144328847, 1211156155, 1480041764, 1195826451, 235841, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.11853, 0.24563, 0.10636, 0.21925, 0.96585, 0.92555, 0.49894, 0.48592, 75, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43477, "SRR6020447", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p02_R2.fastq.gz R5_sec_Trans_p02_R1.fastq.gz", "fastq fastq", 5020749563.0, 33189212.0, "GSM2776988 r2", "0:75.66 1:75.61", "A:1271180542;C:1081665590;G:1257183505;T:1410487545;N:232381", 75, 75, null, null, 1271180542, 1081665590, 1257183505, 1410487545, 232381, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.12477, 0.33055, 0.10671, 0.26254, 0.96773, 0.90583, 0.50071, 0.48529, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43478, "SRR6020448", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p03_R1.fastq.gz R5_sec_Trans_p03_R2.fastq.gz", "fastq fastq", 9930849737.0, 65769125.0, "GSM2776988 r3", "0:75.49 1:75.50", "A:2771601461;C:1594447174;G:1778419273;T:3786066213;N:315616", 75, 75, null, null, 2771601461, 1594447174, 1778419273, 3786066213, 315616, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.31895, 0.74881, 0.28344, 0.57326, 0.96546, 0.85234, 0.4987, 0.52017, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43479, "SRR6020449", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p04_R1.fastq.gz R5_sec_Trans_p04_R2.fastq.gz", "fastq fastq", 7297925579.0, 48343134.0, "GSM2776988 r4", "0:75.51 1:75.45", "A:2157432534;C:1129186071;G:1200823243;T:2810444585;N:39146", 75, 75, null, null, 2157432534, 1129186071, 1200823243, 2810444585, 39146, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.352, 0.75293, 0.31357, 0.60441, 0.95828, 0.83885, 0.50134, 0.50535, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43480, "SRR6020450", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p05_R2.fastq.gz R5_sec_Trans_p05_R1.fastq.gz", "fastq fastq", 13855953318.0, 91804628.0, "GSM2776988 r5", "0:75.50 1:75.43", "A:4146316683;C:2217362039;G:2391706547;T:5100492721;N:75328", 75, 75, null, null, 4146316683, 2217362039, 2391706547, 5100492721, 75328, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.37449, 0.68646, 0.32985, 0.54102, 0.95347, 0.849, 0.49416, 0.50708, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43481, "SRR6020451", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776988", "GSM2776988: R5 sec Trans; Danio rerio; RNA Seq", "GSM2776988", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Trans_p06_R1.fastq.gz R5_sec_Trans_p06_R2.fastq.gz", "fastq fastq", 9723577592.0, 64415623.0, "GSM2776988 r6", "0:75.50 1:75.45", "A:2835431401;C:1511580093;G:1616039076;T:3760473139;N:53883", 75, 75, null, null, 2835431401, 1511580093, 1616039076, 3760473139, 53883, "SRX3171493", "SRS2501302", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.33655, 0.77492, 0.29229, 0.58155, 0.95978, 0.8454, 0.49546, 0.51051, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43482, "SRR6020440", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p01_R1.fastq.gz R5_sec_Scar_p01_R2.fastq.gz", "fastq fastq", 361194076.0, 2376599.0, "GSM2776987 r1", "0:75.99 1:75.99", "A:63932353;C:105212754;G:137339472;T:54692604;N:16893", 75, 75, null, null, 63932353, 105212754, 137339472, 54692604, 16893, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 7e-05, 0.00012, 4e-05, 9e-05, 0.99993, 0.99991, 0.5, 0.75, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43483, "SRR6020441", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p02_R1.fastq.gz R5_sec_Scar_p02_R2.fastq.gz", "fastq fastq", 460055993.0, 3027108.0, "GSM2776987 r2", "0:75.99 1:75.99", "A:80579341;C:134185300;G:175364991;T:69904520;N:21841", 75, 75, null, null, 80579341, 134185300, 175364991, 69904520, 21841, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 5e-05, 2e-05, 2e-05, 0.0, 0.99997, 0.99997, 0.0, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43484, "SRR6020442", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p03_R1.fastq.gz R5_sec_Scar_p03_R2.fastq.gz", "fastq fastq", 466000423.0, 3066554.0, "GSM2776987 r3", "0:75.98 1:75.98", "A:81301391;C:136221817;G:177874701;T:70591092;N:11422", 75, 75, null, null, 81301391, 136221817, 177874701, 70591092, 11422, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0001, 0.00016, 8e-05, 0.00011, 0.99993, 0.99987, 0.0, 0.66666, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43485, "SRR6020443", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p04_R1.fastq.gz R5_sec_Scar_p04_R2.fastq.gz", "fastq fastq", 203843839.0, 1341388.0, "GSM2776987 r4", null, null, null, null, null, null, null, null, null, null, null, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00013, 0.00027, 9e-05, 0.00019, 0.99995, 0.99977, 0.16666, 0.66666, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43486, "SRR6020444", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p05_R1.fastq.gz R5_sec_Scar_p05_R2.fastq.gz", "fastq fastq", 305866297.0, 2012742.0, "GSM2776987 r5", "0:75.98 1:75.98", "A:53459692;C:89448285;G:116312720;T:46644195;N:1405", 75, 75, null, null, 53459692, 89448285, 116312720, 46644195, 1405, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 6e-05, 9e-05, 3e-05, 5e-05, 0.99997, 0.99993, 0.0, 0.5, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43487, "SRR6020445", "SRX3171492", "SRS2501301", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 sec Scar", "GSM2776987", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "GSM2776987", "GSM2776987: R5 sec Scar; Danio rerio; RNA Seq", "GSM2776987", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_sec_Scar_p06_R1.fastq.gz R5_sec_Scar_p06_R2.fastq.gz", "fastq fastq", 557494800.0, 3670391.0, "GSM2776987 r6", "0:75.96 1:75.93", "A:101252524;C:160223186;G:205832526;T:90183664;N:2900", 75, 75, null, null, 101252524, 160223186, 205832526, 90183664, 2900, "SRX3171492", "SRS2501301", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00382, 0.00768, 0.00317, 0.00636, 0.99827, 0.99673, 0.48648, 0.5, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43488, "SRR6020435", "SRX3171491", "SRS2501300", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Trans", "GSM2776986", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "R5 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "GSM2776986", "GSM2776986: R5 prim Trans; Danio rerio; RNA Seq", "GSM2776986", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Trans_p02_R1.fastq.gz R5_prim_Trans_p02_R2.fastq.gz", "fastq fastq", 7812360278.0, 51697480.0, "GSM2776986 r1", "0:75.54 1:75.58", "A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950", 75, 75, null, null, 2098454376, 1641311761, 1943503636, 2128270555, 819950, "SRX3171491", "SRS2501300", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.01048, 0.02593, 0.00847, 0.02007, 0.99614, 0.98742, 0.33227, 0.53419, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43489, "SRR6020436", "SRX3171491", "SRS2501300", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Trans", "GSM2776986", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "R5 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "GSM2776986", "GSM2776986: R5 prim Trans; Danio rerio; RNA Seq", "GSM2776986", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Trans_p03_R1.fastq.gz R5_prim_Trans_p03_R2.fastq.gz", "fastq fastq", 6704494628.0, 44436630.0, "GSM2776986 r2", "0:75.49 1:75.39", "A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167", 75, 75, null, null, 2087008571, 1124579474, 1252171872, 2240541544, 193167, "SRX3171491", "SRS2501300", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.24966, 0.47946, 0.21997, 0.40259, 0.95162, 0.89191, 0.48641, 0.54514, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43490, "SRR6020437", "SRX3171491", "SRS2501300", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Trans", "GSM2776986", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "R5 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "GSM2776986", "GSM2776986: R5 prim Trans; Danio rerio; RNA Seq", "GSM2776986", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Trans_p04_R1.fastq.gz R5_prim_Trans_p04_R2.fastq.gz", "fastq fastq", 8402262674.0, 55692887.0, "GSM2776986 r3", "0:75.48 1:75.39", "A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856", 75, 75, null, null, 2618499207, 1444061167, 1613776766, 2725680678, 244856, "SRX3171491", "SRS2501300", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.26079, 0.43317, 0.23304, 0.36897, 0.95686, 0.90575, 0.50825, 0.53432, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43491, "SRR6020438", "SRX3171491", "SRS2501300", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Trans", "GSM2776986", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "R5 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "GSM2776986", "GSM2776986: R5 prim Trans; Danio rerio; RNA Seq", "GSM2776986", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Trans_p07_R1.fastq.gz R5_prim_Trans_p07_R2.fastq.gz", "fastq fastq", 7045442122.0, 46667895.0, "GSM2776986 r4", "0:75.65 1:75.32", "A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774", 75, 75, null, null, 1992737539, 1481998828, 1584855122, 1984679859, 1170774, "SRX3171491", "SRS2501300", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.08866, 0.20939, 0.07714, 0.18048, 0.97906, 0.95674, 0.50746, 0.52807, 76, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43492, "SRR6020439", "SRX3171491", "SRS2501300", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Trans", "GSM2776986", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "R5 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5", "GSM2776986", "GSM2776986: R5 prim Trans; Danio rerio; RNA Seq", "GSM2776986", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Trans_p08_R1.fastq.gz R5_prim_Trans_p08_R2.fastq.gz", "fastq fastq", 18530449971.0, 122665653.0, "GSM2776986 r5", "0:75.68 1:75.38", "A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121", 75, 75, null, null, 4667348302, 4333487274, 4681098112, 4848415162, 101121, "SRX3171491", "SRS2501300", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.05599, 0.12252, 0.04627, 0.10255, 0.98409, 0.96467, 0.50898, 0.5274, 75, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43493, "SRR6020429", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p01_R1.fastq.gz R5_prim_Scar_p01_R2.fastq.gz", "fastq fastq", 24766319.0, 163126.0, "GSM2776985 r1", "0:75.95 1:75.87", "A:4693411;C:6959422;G:8727578;T:4381992;N:3916", 75, 75, null, null, 4693411, 6959422, 8727578, 4381992, 3916, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00023, 0.00064, 0.00018, 0.00044, 0.99989, 0.99969, 0.6, 0.8, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43494, "SRR6020430", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p02_R1.fastq.gz R5_prim_Scar_p02_R2.fastq.gz", "fastq fastq", 1266120923.0, 8332017.0, "GSM2776985 r2", "0:75.98 1:75.98", "A:222649072;C:369728088;G:482809574;T:190903334;N:30855", 75, 75, null, null, 222649072, 369728088, 482809574, 190903334, 30855, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 4e-05, 2e-05, 3e-05, 1e-05, 0.99997, 0.99997, 0.0, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43495, "SRR6020431", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p03_R1.fastq.gz R5_prim_Scar_p03_R2.fastq.gz", "fastq fastq", 494949145.0, 3257351.0, "GSM2776985 r3", "0:75.98 1:75.97", "A:87163836;C:143707892;G:188542837;T:75522642;N:11938", 75, 75, null, null, 87163836, 143707892, 188542837, 75522642, 11938, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00015, 5e-05, 9e-05, 2e-05, 0.99995, 0.99993, 0.0, 0.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43496, "SRR6020432", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p04_R1.fastq.gz R5_prim_Scar_p04_R2.fastq.gz", "fastq fastq", 376701290.0, 2478856.0, "GSM2776985 r4", "0:75.99 1:75.98", "A:66002492;C:109979363;G:143811826;T:56905698;N:1911", 75, 75, null, null, 66002492, 109979363, 143811826, 56905698, 1911, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 4e-05, 5e-05, 3e-05, 4e-05, 1.0, 1.0, null, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43497, "SRR6020433", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p07_R1.fastq.gz R5_prim_Scar_p07_R2.fastq.gz", "fastq fastq", 34956996.0, 230152.0, "GSM2776985 r5", "0:75.96 1:75.92", "A:6443422;C:10072498;G:12853211;T:5583477;N:4388", 75, 75, null, null, 6443422, 10072498, 12853211, 5583477, 4388, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00459, 0.01152, 0.00401, 0.00964, 0.99821, 0.99624, 0.43333, 0.53588, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43498, "SRR6020434", "SRX3171490", "SRS2501299", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R5 prim Scar", "GSM2776985", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "R5 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6", "GSM2776985", "GSM2776985: R5 prim Scar; Danio rerio; RNA Seq", "GSM2776985", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R5_prim_Scar_p08_R1.fastq.gz R5_prim_Scar_p08_R2.fastq.gz", "fastq fastq", 833299107.0, 5483661.0, "GSM2776985 r6", "0:75.98 1:75.98", "A:145414972;C:243570136;G:319061924;T:125238697;N:13378", 75, 75, null, null, 145414972, 243570136, 319061924, 125238697, 13378, "SRX3171490", "SRS2501299", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 6e-05, 8e-05, 2e-05, 3e-05, 0.99991, 0.99989, 0.75, 0.8, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43507, "SRR6020417", "SRX3171487", "SRS2501295", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Trans", "GSM2776982", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776982", "GSM2776982: R4 terv Trans; Danio rerio; RNA Seq", "GSM2776982", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Trans_p01_R1.fastq.gz R4_terv_Trans_p01_R2.fastq.gz", "fastq fastq", 899878376.0, 5966262.0, "GSM2776982 r1", "0:75.45 1:75.38", "A:292042567;C:146271033;G:139925382;T:321623997;N:15397", 75, 75, null, null, 292042567, 146271033, 139925382, 321623997, 15397, "SRX3171487", "SRS2501295", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.33677, 0.59727, 0.29432, 0.51752, 0.95641, 0.92176, 0.48959, 0.52071, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43508, "SRR6020418", "SRX3171487", "SRS2501295", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Trans", "GSM2776982", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776982", "GSM2776982: R4 terv Trans; Danio rerio; RNA Seq", "GSM2776982", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Trans_p02_R2.fastq.gz R4_terv_Trans_p02_R1.fastq.gz", "fastq fastq", 8835694041.0, 58517949.0, "GSM2776982 r2", "0:75.51 1:75.48", "A:2524661133;C:1502485662;G:1635422368;T:3172516743;N:608135", 75, 75, null, null, 2524661133, 1502485662, 1635422368, 3172516743, 608135, "SRX3171487", "SRS2501295", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.37169, 0.69933, 0.33104, 0.59253, 0.93659, 0.82836, 0.49319, 0.51176, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43509, "SRR6020419", "SRX3171487", "SRS2501295", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Trans", "GSM2776982", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776982", "GSM2776982: R4 terv Trans; Danio rerio; RNA Seq", "GSM2776982", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Trans_p03_R1.fastq.gz R4_terv_Trans_p03_R2.fastq.gz", "fastq fastq", 4386400893.0, 29067702.0, "GSM2776982 r3", "0:75.49 1:75.41", "A:1326956065;C:724491767;G:749677156;T:1585148439;N:127466", 75, 75, null, null, 1326956065, 724491767, 749677156, 1585148439, 127466, "SRX3171487", "SRS2501295", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.31136, 0.62851, 0.26305, 0.46553, 0.95517, 0.87024, 0.52178, 0.52923, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43510, "SRR6020420", "SRX3171487", "SRS2501295", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Trans", "GSM2776982", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776982", "GSM2776982: R4 terv Trans; Danio rerio; RNA Seq", "GSM2776982", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Trans_p04_R1.fastq.gz R4_terv_Trans_p04_R2.fastq.gz", "fastq fastq", 9245152121.0, 61263899.0, "GSM2776982 r4", "0:75.46 1:75.45", "A:2833957542;C:1482543934;G:1582652549;T:3345945412;N:52684", 75, 75, null, null, 2833957542, 1482543934, 1582652549, 3345945412, 52684, "SRX3171487", "SRS2501295", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.33283, 0.69016, 0.28123, 0.49239, 0.95039, 0.83437, 0.49598, 0.54367, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43511, "SRR6020413", "SRX3171486", "SRS2501296", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Scar", "GSM2776981", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776981", "GSM2776981: R4 terv Scar; Danio rerio; RNA Seq", "GSM2776981", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Scar_p01_R1.fastq.gz R4_terv_Scar_p01_R2.fastq.gz", "fastq fastq", 63013537.0, 414730.0, "GSM2776981 r1", "0:75.98 1:75.96", "A:11340679;C:18348371;G:23382873;T:9940711;N:903", 75, 75, null, null, 11340679, 18348371, 23382873, 9940711, 903, "SRX3171486", "SRS2501296", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0005, 0.0001, 0.00026, 7e-05, 0.99993, 0.99995, 0.05882, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43512, "SRR6020414", "SRX3171486", "SRS2501296", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Scar", "GSM2776981", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776981", "GSM2776981: R4 terv Scar; Danio rerio; RNA Seq", "GSM2776981", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Scar_p02_R1.fastq.gz R4_terv_Scar_p02_R2.fastq.gz", "fastq fastq", 118778173.0, 782191.0, "GSM2776981 r2", "0:75.93 1:75.92", "A:22484503;C:33087570;G:42161784;T:21035442;N:8874", 75, 75, null, null, 22484503, 33087570, 42161784, 21035442, 8874, "SRX3171486", "SRS2501296", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.02075, 0.05067, 0.01832, 0.04276, 0.99279, 0.97654, 0.44392, 0.52218, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43513, "SRR6020415", "SRX3171486", "SRS2501296", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Scar", "GSM2776981", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776981", "GSM2776981: R4 terv Scar; Danio rerio; RNA Seq", "GSM2776981", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Scar_p03_R1.fastq.gz R4_terv_Scar_p03_R2.fastq.gz", "fastq fastq", 713249164.0, 4694227.0, "GSM2776981 r3", "0:75.98 1:75.96", "A:125818684;C:207435216;G:268732472;T:111244414;N:18378", 75, 75, null, null, 125818684, 207435216, 268732472, 111244414, 18378, "SRX3171486", "SRS2501296", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 1e-05, 1e-05, 0.0, 0.99997, 1.0, 0.0, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43514, "SRR6020416", "SRX3171486", "SRS2501296", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terv Scar", "GSM2776981", null, "source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terv Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary ventral fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776981", "GSM2776981: R4 terv Scar; Danio rerio; RNA Seq", "GSM2776981", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terv_Scar_p04_R1.fastq.gz R4_terv_Scar_p04_R2.fastq.gz", "fastq fastq", 483844486.0, 3184595.0, "GSM2776981 r4", "0:75.98 1:75.95", "A:85646205;C:140894435;G:180981122;T:76320328;N:2396", 75, 75, null, null, 85646205, 140894435, 180981122, 76320328, 2396, "SRX3171486", "SRS2501296", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0003, 0.00067, 0.00018, 0.00046, 0.99989, 0.99935, 0.15, 0.41176, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43515, "SRR6020409", "SRX3171485", "SRS2501294", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Trans", "GSM2776980", null, "source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776980", "GSM2776980: R4 terd Trans; Danio rerio; RNA Seq", "GSM2776980", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Trans_p01_R1.fastq.gz R4_terd_Trans_p01_R2.fastq.gz", "fastq fastq", 9353477829.0, 61985103.0, "GSM2776980 r1", "0:75.45 1:75.45", "A:2918476093;C:1414091678;G:1474868294;T:3545988622;N:53142", 75, 75, null, null, 2918476093, 1414091678, 1474868294, 3545988622, 53142, "SRX3171485", "SRS2501294", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.36441, 0.7593, 0.31336, 0.55295, 0.95093, 0.82292, 0.49914, 0.53019, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43516, "SRR6020410", "SRX3171485", "SRS2501294", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Trans", "GSM2776980", null, "source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776980", "GSM2776980: R4 terd Trans; Danio rerio; RNA Seq", "GSM2776980", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Trans_p02_R1.fastq.gz R4_terd_Trans_p02_R2.fastq.gz", "fastq fastq", 6626365664.0, 43908545.0, "GSM2776980 r2", "0:75.44 1:75.47", "A:1980665411;C:1019945066;G:1082628078;T:2543089101;N:38008", 75, 75, null, null, 1980665411, 1019945066, 1082628078, 2543089101, 38008, "SRX3171485", "SRS2501294", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.32749, 0.78639, 0.25705, 0.43545, 0.95745, 0.82, 0.5, 0.52298, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43517, "SRR6020411", "SRX3171485", "SRS2501294", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Trans", "GSM2776980", null, "source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776980", "GSM2776980: R4 terd Trans; Danio rerio; RNA Seq", "GSM2776980", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Trans_p03_R1.fastq.gz R4_terd_Trans_p03_R2.fastq.gz", "fastq fastq", 250213383.0, 1657189.0, "GSM2776980 r3", "0:75.51 1:75.48", "A:70872645;C:40721033;G:44641734;T:93961355;N:16616", 75, 75, null, null, 70872645, 40721033, 44641734, 93961355, 16616, "SRX3171485", "SRS2501294", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.39985, 0.75081, 0.34725, 0.58284, 0.93975, 0.82116, 0.49709, 0.51312, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43518, "SRR6020412", "SRX3171485", "SRS2501294", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Trans", "GSM2776980", null, "source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "tertiary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776980", "GSM2776980: R4 terd Trans; Danio rerio; RNA Seq", "GSM2776980", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Trans_p04_R1.fastq.gz R4_terd_Trans_p04_R2.fastq.gz", "fastq fastq", 2439737928.0, 16175327.0, "GSM2776980 r4", "0:75.43 1:75.40", "A:791363066;C:393366804;G:387269134;T:867699009;N:39915", 75, 75, null, null, 791363066, 393366804, 387269134, 867699009, 39915, "SRX3171485", "SRS2501294", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.41064, 0.68389, 0.36279, 0.60184, 0.94801, 0.91321, 0.50483, 0.5018, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43519, "SRR6020405", "SRX3171484", "SRS2501293", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Scar", "GSM2776979", null, "source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "teritary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776979", "GSM2776979: R4 terd Scar; Danio rerio; RNA Seq", "GSM2776979", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776979", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Scar_p01_R1.fastq.gz R4_terd_Scar_p01_R2.fastq.gz", "fastq fastq", 472339159.0, 3108723.0, "GSM2776979 r1", "0:75.98 1:75.96", "A:83061434;C:137317024;G:178719638;T:73238676;N:2387", 75, 75, null, null, 83061434, 137317024, 178719638, 73238676, 2387, "SRX3171484", "SRS2501293", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00033, 0.00025, 0.0002, 0.00013, 0.99993, 0.99963, 0.0, 0.61111, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43520, "SRR6020406", "SRX3171484", "SRS2501293", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Scar", "GSM2776979", null, "source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "teritary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776979", "GSM2776979: R4 terd Scar; Danio rerio; RNA Seq", "GSM2776979", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776979", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Scar_p02_R1.fastq.gz R4_terd_Scar_p02_R2.fastq.gz", "fastq fastq", 405913408.0, 2671239.0, "GSM2776979 r2", "0:75.99 1:75.97", "A:71703296;C:117980100;G:153764667;T:62463222;N:2123", 75, 75, null, null, 71703296, 117980100, 153764667, 62463222, 2123, "SRX3171484", "SRS2501293", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 0.00011, 1e-05, 4e-05, 0.99993, 0.99981, 0.66666, 0.7, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43521, "SRR6020407", "SRX3171484", "SRS2501293", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Scar", "GSM2776979", null, "source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "teritary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776979", "GSM2776979: R4 terd Scar; Danio rerio; RNA Seq", "GSM2776979", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776979", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Scar_p03_R1.fastq.gz R4_terd_Scar_p03_R2.fastq.gz", "fastq fastq", 35300008.0, 232328.0, "GSM2776979 r3", "0:75.97 1:75.97", "A:6443488;C:10004950;G:13144621;T:5704811;N:2138", 75, 75, null, null, 6443488, 10004950, 13144621, 5704811, 2138, "SRX3171484", "SRS2501293", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00275, 0.00097, 0.00214, 0.00083, 0.99943, 0.99955, 0.15454, 0.52173, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43522, "SRR6020408", "SRX3171484", "SRS2501293", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 terd Scar", "GSM2776979", null, "source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "R4 terd Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "teritary dorsal fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4", "GSM2776979", "GSM2776979: R4 terd Scar; Danio rerio; RNA Seq", "GSM2776979", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776979", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_terd_Scar_p04_R1.fastq.gz R4_terd_Scar_p04_R2.fastq.gz", "fastq fastq", 35300008.0, 232328.0, "GSM2776979 r4", "0:75.97 1:75.97", "A:6443488;C:10004950;G:13144621;T:5704811;N:2138", 75, 75, null, null, 6443488, 10004950, 13144621, 5704811, 2138, "SRX3171484", "SRS2501293", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00276, 0.00097, 0.00213, 0.00082, 0.99945, 0.99949, 0.14035, 0.53846, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43523, "SRR6020399", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p01_R1.fastq.gz R4_sec_Trans_p01_R2.fastq.gz", "fastq fastq", 7943223694.0, 52632584.0, "GSM2776978 r1", "0:75.50 1:75.42", "A:2426047253;C:1345760701;G:1411992441;T:2757726644;N:1696655", 75, 75, null, null, 2426047253, 1345760701, 1411992441, 2757726644, 1696655, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.39936, 0.64405, 0.35361, 0.55608, 0.91311, 0.84431, 0.5165, 0.52376, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43524, "SRR6020400", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p02_R1.fastq.gz R4_sec_Trans_p02_R2.fastq.gz", "fastq fastq", 8875571511.0, 58802279.0, "GSM2776978 r2", "0:75.52 1:75.42", "A:2702312372;C:1527849144;G:1608513066;T:3034988415;N:1908514", 75, 75, null, null, 2702312372, 1527849144, 1608513066, 3034988415, 1908514, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.38955, 0.61673, 0.34428, 0.5327, 0.91774, 0.85094, 0.50279, 0.51953, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43525, "SRR6020401", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p03_R1.fastq.gz R4_sec_Trans_p03_R2.fastq.gz", "fastq fastq", 10196306186.0, 67549716.0, "GSM2776978 r3", "0:75.48 1:75.47", "A:3021055822;C:1591602601;G:1717130650;T:3866184067;N:333046", 75, 75, null, null, 3021055822, 1591602601, 1717130650, 3866184067, 333046, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.42177, 0.73274, 0.37881, 0.60342, 0.93845, 0.83104, 0.49961, 0.48288, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43526, "SRR6020402", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p04_R1.fastq.gz R4_sec_Trans_p04_R2.fastq.gz", "fastq fastq", 16321632703.0, 108129317.0, "GSM2776978 r4", "0:75.48 1:75.47", "A:4839288181;C:2524952022;G:2722722795;T:6234157991;N:511714", 75, 75, null, null, 4839288181, 2524952022, 2722722795, 6234157991, 511714, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.43062, 0.74617, 0.38255, 0.59574, 0.93693, 0.8256, 0.50653, 0.53888, 76, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43527, "SRR6020403", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p05_R1.fastq.gz R4_sec_Trans_p05_R2.fastq.gz", "fastq fastq", 8368447970.0, 55444521.0, "GSM2776978 r5", "0:75.47 1:75.46", "A:2470524458;C:1322545235;G:1459320910;T:3115796506;N:260861", 75, 75, null, null, 2470524458, 1322545235, 1459320910, 3115796506, 260861, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.38066, 0.70664, 0.33844, 0.56193, 0.94134, 0.82846, 0.48774, 0.47937, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43528, "SRR6020404", "SRX3171483", "SRS2501292", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Trans", "GSM2776978", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776978", "GSM2776978: R4 sec Trans; Danio rerio; RNA Seq", "GSM2776978", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776978", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Trans_p06_R1.fastq.gz R4_sec_Trans_p06_R2.fastq.gz", "fastq fastq", 9774461624.0, 64760766.0, "GSM2776978 r6", "0:75.47 1:75.46", "A:2902527714;C:1488941576;G:1661506049;T:3721177113;N:309172", 75, 75, null, null, 2902527714, 1488941576, 1661506049, 3721177113, 309172, "SRX3171483", "SRS2501292", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.39334, 0.71354, 0.35122, 0.56253, 0.94513, 0.84628, 0.47779, 0.55996, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43529, "SRR6020393", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p01_R1.fastq.gz R4_sec_Scar_p01_R2.fastq.gz", "fastq fastq", 443752860.0, 2921141.0, "GSM2776977 r1", "0:75.98 1:75.93", "A:78584919;C:129545943;G:166851959;T:68680115;N:89924", 75, 75, null, null, 78584919, 129545943, 166851959, 68680115, 89924, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00014, 0.00018, 9e-05, 0.00013, 0.99991, 0.99985, 0.4, 0.57142, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43530, "SRR6020394", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p02_R1.fastq.gz R4_sec_Scar_p02_R2.fastq.gz", "fastq fastq", 609377510.0, 4011701.0, "GSM2776977 r2", "0:75.99 1:75.91", "A:108185883;C:176784326;G:229824363;T:94453370;N:129568", 75, 75, null, null, 108185883, 176784326, 229824363, 94453370, 129568, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 6e-05, 0.0001, 5e-05, 7e-05, 1.0, 0.99991, null, 0.25, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43531, "SRR6020395", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p03_R1.fastq.gz R4_sec_Scar_p03_R2.fastq.gz", "fastq fastq", 695786067.0, 4580703.0, "GSM2776977 r3", "0:75.98 1:75.91", "A:122056429;C:202686271;G:262426973;T:108597814;N:18580", 75, 75, null, null, 122056429, 202686271, 262426973, 108597814, 18580, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00035, 0.00084, 0.00028, 0.00068, 0.99981, 0.99955, 0.18181, 0.45454, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43532, "SRR6020396", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p04_R1.fastq.gz R4_sec_Scar_p04_R2.fastq.gz", "fastq fastq", 468236053.0, 3082347.0, "GSM2776977 r4", "0:75.98 1:75.92", "A:82822403;C:136423938;G:175959465;T:73018299;N:11948", 75, 75, null, null, 82822403, 136423938, 175959465, 73018299, 11948, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 7e-05, 1e-05, 3e-05, 0.99997, 0.99991, 0.0, 0.75, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43533, "SRR6020397", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p05_R1.fastq.gz R4_sec_Scar_p05_R2.fastq.gz", "fastq fastq", 494012269.0, 3251619.0, "GSM2776977 r5", "0:75.98 1:75.94", "A:87398485;C:143668568;G:186485697;T:76445953;N:13566", 75, 75, null, null, 87398485, 143668568, 186485697, 76445953, 13566, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 8e-05, 7e-05, 4e-05, 1e-05, 0.99991, 0.99985, 0.2, 0.71428, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43534, "SRR6020398", "SRX3171482", "SRS2501291", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 sec Scar", "GSM2776977", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "R4 sec Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "secondary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6", "GSM2776977", "GSM2776977: R4 sec Scar; Danio rerio; RNA Seq", "GSM2776977", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776977", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_sec_Scar_p06_R1.fastq.gz R4_sec_Scar_p06_R2.fastq.gz", "fastq fastq", 488664520.0, 3216541.0, "GSM2776977 r6", "0:75.98 1:75.94", "A:86623588;C:141946345;G:183757005;T:76325350;N:12232", 75, 75, null, null, 86623588, 141946345, 183757005, 76325350, 12232, "SRX3171482", "SRS2501291", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0001, 0.00015, 5e-05, 8e-05, 0.99991, 0.99983, 0.16666, 0.75, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43535, "SRR6020387", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p01_R1.fastq.gz R4_prim_Trans_p01_R2.fastq.gz", "fastq fastq", 4156649914.0, 27498834.0, "GSM2776976 r1", "0:75.66 1:75.50", "A:1184667722;C:812111779;G:946047137;T:1213491214;N:332062", 75, 75, null, null, 1184667722, 812111779, 946047137, 1213491214, 332062, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.13191, 0.27606, 0.11079, 0.21313, 0.97981, 0.95864, 0.48952, 0.51323, 76, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43536, "SRR6020388", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p02_R1.fastq.gz R4_prim_Trans_p02_R2.fastq.gz", "fastq fastq", 5961095878.0, 39431358.0, "GSM2776976 r2", "0:75.66 1:75.51", "A:1678045732;C:1185915367;G:1391829821;T:1704836561;N:468397", 75, 75, null, null, 1678045732, 1185915367, 1391829821, 1704836561, 468397, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.13017, 0.27029, 0.11004, 0.21778, 0.9795, 0.95978, 0.54044, 0.51146, 76, 76, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43537, "SRR6020389", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p03_R1.fastq.gz R4_prim_Trans_p03_R2.fastq.gz", "fastq fastq", 6170232577.0, 40846092.0, "GSM2776976 r3", "0:75.56 1:75.50", "A:1866777846;C:1148020988;G:1151073641;T:2003993265;N:366837", 75, 75, null, null, 1866777846, 1148020988, 1151073641, 2003993265, 366837, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.21204, 0.40881, 0.18286, 0.33189, 0.95931, 0.9108, 0.49141, 0.53253, 75, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43538, "SRR6020390", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p04_R1.fastq.gz R4_prim_Trans_p04_R2.fastq.gz", "fastq fastq", 11725606474.0, 77611342.0, "GSM2776976 r4", "0:75.62 1:75.46", "A:3255674293;C:2567072026;G:2847190480;T:3054954945;N:714730", 75, 75, null, null, 3255674293, 2567072026, 2847190480, 3054954945, 714730, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.06986, 0.13983, 0.05982, 0.11888, 0.98516, 0.97161, 0.49686, 0.4638, 75, 75, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43539, "SRR6020391", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p05_R1.fastq.gz R4_prim_Trans_p05_R2.fastq.gz", "fastq fastq", 10721896827.0, 71080622.0, "GSM2776976 r5", "0:75.44 1:75.41", "A:3568478635;C:1747554798;G:1675757438;T:3729472140;N:633816", 75, 75, null, null, 3568478635, 1747554798, 1675757438, 3729472140, 633816, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.32298, 0.52706, 0.28009, 0.43701, 0.94349, 0.90078, 0.51345, 0.52304, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43540, "SRR6020392", "SRX3171481", "SRS2501290", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Trans", "GSM2776976", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Trans", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776976", "GSM2776976: R4 prim Trans; Danio rerio; RNA Seq", "GSM2776976", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776976", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Trans_p06_R1.fastq.gz R4_prim_Trans_p06_R2.fastq.gz", "fastq fastq", 4861560177.0, 32218130.0, "GSM2776976 r6", "0:75.46 1:75.44", "A:1606516776;C:766379277;G:687731226;T:1800636189;N:296709", 75, 75, null, null, 1606516776, 766379277, 687731226, 1800636189, 296709, "SRX3171481", "SRS2501290", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.40198, 0.66219, 0.35056, 0.55779, 0.94671, 0.8913, 0.48395, 0.50179, 75, 75, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43541, "SRR6020381", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p01_R1.fastq.gz R4_prim_Scar_p01_R2.fastq.gz", "fastq fastq", 2115181733.0, 13930610.0, "GSM2776975 r1", "0:75.96 1:75.88", "A:379992687;C:608145647;G:806462037;T:320430832;N:150530", 75, 75, null, null, 379992687, 608145647, 806462037, 320430832, 150530, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 4e-05, 2e-05, 2e-05, 1.0, 0.99997, null, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43542, "SRR6020382", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p02_R1.fastq.gz R4_prim_Scar_p02_R2.fastq.gz", "fastq fastq", 1500850853.0, 9884525.0, "GSM2776975 r2", "0:75.96 1:75.88", "A:272764495;C:429257065;G:572879423;T:225831427;N:118443", 75, 75, null, null, 272764495, 429257065, 572879423, 225831427, 118443, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0, 3e-05, 0.0, 1e-05, 1.0, 0.99997, null, 0.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43543, "SRR6020383", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p03_R1.fastq.gz R4_prim_Scar_p03_R2.fastq.gz", "fastq fastq", 1802726164.0, 11867972.0, "GSM2776975 r3", "0:75.98 1:75.91", "A:320691778;C:528568175;G:676214104;T:277152518;N:99589", 75, 75, null, null, 320691778, 528568175, 676214104, 277152518, 99589, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 1e-05, 0.0, 0.0, 0.0, 1.0, 1.0, null, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43544, "SRR6020384", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p04_R1.fastq.gz R4_prim_Scar_p04_R2.fastq.gz", "fastq fastq", 1589218979.0, 10459351.0, "GSM2776975 r4", "0:75.98 1:75.96", "A:284759473;C:465370937;G:594649808;T:244354408;N:84353", 75, 75, null, null, 284759473, 465370937, 594649808, 244354408, 84353, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 8e-05, 2e-05, 6e-05, 0.99997, 0.99997, 0.0, 1.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43545, "SRR6020385", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p05_R1.fastq.gz R4_prim_Scar_p05_R2.fastq.gz", "fastq fastq", 1044289567.0, 6872484.0, "GSM2776975 r5", "0:75.99 1:75.97", "A:180521535;C:302898685;G:398946567;T:161866241;N:56539", 75, 75, null, null, 180521535, 302898685, 398946567, 161866241, 56539, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0, 2e-05, 0.0, 1e-05, 1.0, 1.0, null, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43546, "SRR6020386", "SRX3171480", "SRS2501289", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.", null, "pubmed:29590089", null, "R4 prim Scar", "GSM2776975", null, "source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "R4 prim Scar", "In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6", "GSM2776975", "GSM2776975: R4 prim Scar; Danio rerio; RNA Seq", "GSM2776975", null, "1", "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM2776975", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "R4_prim_Scar_p06_R1.fastq.gz R4_prim_Scar_p06_R2.fastq.gz", "fastq fastq", 1191573683.0, 7850142.0, "GSM2776975 r6", "0:75.98 1:75.81", "A:222979447;C:342633187;G:444672356;T:181222920;N:65773", 75, 75, null, null, 222979447, 342633187, 444672356, 181222920, 65773, "SRX3171480", "SRS2501289", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 3e-05, 0.0, 1e-05, 0.0, 0.99997, 1.0, 1.0, null, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-09-08", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43623, "SRR5961766", "SRX3119877", "SRS2454736", "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.", null, "pubmed:29590089", null, "P1 primary fin Scars", "GSM2752200", null, "source name:primary fin single cells|cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2", "P1 primary fin 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", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2", "GSM2752200", "GSM2752200: P1 primary fin Scars; Danio rerio; RNA Seq", "GSM2752200", null, "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:GSM2752200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P1_fin_Scar_p01_R1.fastq.gz P1_fin_Scar_p01_R2.fastq.gz", "fastq fastq", 295970986.0, 1947440.0, "GSM2752200 r1", "0:75.99 1:75.99", "A:52888700;C:85164846;G:110699732;T:47204092;N:13616", 75, 75, null, null, 52888700, 85164846, 110699732, 47204092, 13616, "SRX3119877", "SRS2454736", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 4e-05, 3e-05, 2e-05, 0.0, 0.99995, 0.99991, 0.5, 0.25, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2017-08-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43624, "SRR5961767", "SRX3119877", "SRS2454736", "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.", null, "pubmed:29590089", null, "P1 primary fin Scars", "GSM2752200", null, "source name:primary fin single cells|cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2", "P1 primary fin 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", "primary fin single cells", null, "post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2", "GSM2752200", "GSM2752200: P1 primary fin Scars; Danio rerio; RNA Seq", "GSM2752200", null, "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:GSM2752200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P1_fin_Scar_p02_R1.fastq.gz P1_fin_Scar_p02_R2.fastq.gz", "fastq fastq", 663461589.0, 4365910.0, "GSM2752200 r2", "0:75.98 1:75.99", "A:121052549;C:188284261;G:244595786;T:109498791;N:30202", 75, 75, null, null, 121052549, 188284261, 244595786, 109498791, 30202, "SRX3119877", "SRS2454736", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00271, 0.00078, 0.00264, 0.00075, 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", null, "Netherlands", "2017-08-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 69, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], 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[submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "scartrace", "p2": "Surface Structure"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=scartrace&tissue_curation_coarse=Surface+Structure", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=scartrace&tissue_curation_coarse=Surface+Structure&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": 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