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