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
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
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
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
43603,SRR6020324,SRX3171465,SRS2501274,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 right midbrain Trans,GSM2776960,,source name:right midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:right midbrain|sorted plates:1,R1 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:R1|tissue:right midbrain|sorted plates:1,GSM2776960,GSM2776960: R1 right midbrain Trans; Danio rerio; RNA Seq,GSM2776960,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776960,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_right-midbrain_Trans_p01_R1.fastq.gz R1_right-midbrain_Trans_p01_R2.fastq.gz,fastq fastq,17638707252.0,116700151.0,GSM2776960 r1,0:75.73 1:75.42,A:4244828767;C:4448502500;G:4757618770;T:4183990981;N:3766234,75,75,,,4244828767,4448502500,4757618770,4183990981,3766234,SRX3171465,SRS2501274,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00363,0.00999,0.00296,0.00784,0.99841,0.99523,0.4421,0.50943,74,76,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
43604,SRR6020323,SRX3171464,SRS2501273,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 right midbrain Scar,GSM2776959,,source name:right midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:right midbrain|sorted plates:1,R1 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:R1|tissue:right midbrain|sorted plates:1,GSM2776959,GSM2776959: R1 right midbrain Scar; Danio rerio; RNA Seq,GSM2776959,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776959,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_right-midbrain_Scar_p01_R1.fastq.gz R1_right-midbrain_Scar_p01_R2.fastq.gz,fastq fastq,1241105393.0,8168179.0,GSM2776959 r1,0:75.98 1:75.96,A:223665309;C:363340751;G:462620263;T:191351747;N:127323,75,75,,,223665309,363340751,462620263,191351747,127323,SRX3171464,SRS2501273,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0002,5e-05,0.00016,3e-05,0.99995,0.99997,0.33333,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Brain,Nervous System
43607,SRR6020319,SRX3171461,SRS2501270,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 left midbrain Trans,GSM2776956,,source name:midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:left midbrain|sorted plates:2,R1 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.,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:R1|tissue:left midbrain|sorted plates:2,GSM2776956,GSM2776956: R1 left midbrain Trans; Danio rerio; RNA Seq,GSM2776956,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776956,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_left-midbrain_Trans_p01_R2.fastq.gz R1_left-midbrain_Trans_p01_R1.fastq.gz,fastq fastq,4445540386.0,29419746.0,GSM2776956 r1,0:75.64 1:75.47,A:1335587831;C:878932302;G:897654367;T:1332402402;N:963484,75,75,,,1335587831,878932302,897654367,1332402402,963484,SRX3171461,SRS2501270,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.05752,0.17176,0.03479,0.10404,0.98364,0.94836,0.30195,0.48669,76,76,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,Brain,Nervous System
43608,SRR6020320,SRX3171461,SRS2501270,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 left midbrain Trans,GSM2776956,,source name:midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:left midbrain|sorted plates:2,R1 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.,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:R1|tissue:left midbrain|sorted plates:2,GSM2776956,GSM2776956: R1 left midbrain Trans; Danio rerio; RNA Seq,GSM2776956,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776956,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_left-midbrain_Trans_p02_R2.fastq.gz R1_left-midbrain_Trans_p02_R1.fastq.gz,fastq fastq,8855752696.0,58533726.0,GSM2776956 r2,0:75.73 1:75.56,A:2205336012;C:2049004496;G:2330370320;T:2270043321;N:998547,75,75,,,2205336012,2049004496,2330370320,2270043321,998547,SRX3171461,SRS2501270,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.03452,0.12353,0.02791,0.08015,0.99044,0.95294,0.37305,0.48849,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Brain,Nervous System
43609,SRR6020317,SRX3171460,SRS2501269,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 left midbrain Scar,GSM2776955,,source name:midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:left midbrain|sorted plates:2,R1 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.,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:R1|tissue:left midbrain|sorted plates:2,GSM2776955,GSM2776955: R1 left midbrain Scar; Danio rerio; RNA Seq,GSM2776955,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_left-midbrain_Scar_p01_R1.fastq.gz R1_left-midbrain_Scar_p01_R2.fastq.gz,fastq fastq,570350357.0,3754845.0,GSM2776955 r1,0:75.98 1:75.92,A:102634901;C:167765914;G:211752350;T:88082552;N:114640,75,75,,,102634901,167765914,211752350,88082552,114640,SRX3171460,SRS2501269,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00012,1e-05,8e-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,Brain,Nervous System
43610,SRR6020318,SRX3171460,SRS2501269,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 left midbrain Scar,GSM2776955,,source name:midbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:left midbrain|sorted plates:2,R1 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.,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:R1|tissue:left midbrain|sorted plates:2,GSM2776955,GSM2776955: R1 left midbrain Scar; Danio rerio; RNA Seq,GSM2776955,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_left-midbrain_Scar_p02_R1.fastq.gz R1_left-midbrain_Scar_p02_R2.fastq.gz,fastq fastq,1556431864.0,10243404.0,GSM2776955 r2,0:75.98 1:75.96,A:277122421;C:452203041;G:585437274;T:241507312;N:161816,75,75,,,277122421,452203041,585437274,241507312,161816,SRX3171460,SRS2501269,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,0.0,1e-05,0.0,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Brain,Nervous System
43615,SRR6020311,SRX3171457,SRS2501267,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 hindbrain Trans,GSM2776952,,source name:hindbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:hindbrain|sorted plates:2,R1 hindbrain 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.,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:R1|tissue:hindbrain|sorted plates:2,GSM2776952,GSM2776952: R1 hindbrain Trans; Danio rerio; RNA Seq,GSM2776952,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_hindbrain_Trans_p01_R1.fastq.gz R1_hindbrain_Trans_p01_R2.fastq.gz,fastq fastq,5469421141.0,36247476.0,GSM2776952 r1,0:75.42 1:75.48,A:1608427140;C:1103451553;G:1290351319;T:1466941558;N:249571,75,75,,,1608427140,1103451553,1290351319,1466941558,249571,SRX3171457,SRS2501267,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01887,0.03727,0.01341,0.0229,0.99328,0.98096,0.28165,0.36186,76,76,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
43616,SRR6020312,SRX3171457,SRS2501267,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 hindbrain Trans,GSM2776952,,source name:hindbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:hindbrain|sorted plates:2,R1 hindbrain 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.,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:R1|tissue:hindbrain|sorted plates:2,GSM2776952,GSM2776952: R1 hindbrain Trans; Danio rerio; RNA Seq,GSM2776952,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_hindbrain_Trans_p02_R1.fastq.gz R1_hindbrain_Trans_p02_R2.fastq.gz,fastq fastq,12370235768.0,81804808.0,GSM2776952 r2,0:75.72 1:75.50,A:3099355621;C:2882274178;G:3344412870;T:3042147246;N:2045853,75,75,,,3099355621,2882274178,3344412870,3042147246,2045853,SRX3171457,SRS2501267,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01079,0.03706,0.00756,0.02196,0.99504,0.97751,0.32286,0.39205,75,75,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
43617,SRR6020309,SRX3171456,SRS2501265,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 hindbrain Scar,GSM2776951,,source name:hindbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:hindbrain|sorted plates:2,R1 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:R1|tissue:hindbrain|sorted plates:2,GSM2776951,GSM2776951: R1 hindbrain Scar; Danio rerio; RNA Seq,GSM2776951,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776951,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_hindbrain_Scar_p01_R1.fastq.gz R1_hindbrain_Scar_p01_R2.fastq.gz,fastq fastq,34200621.0,225214.0,GSM2776951 r1,0:75.98 1:75.88,A:6193230;C:9909031;G:12495930;T:5600985;N:1445,75,75,,,6193230,9909031,12495930,5600985,1445,SRX3171456,SRS2501265,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00058,0.00137,0.00038,0.00091,0.99943,0.9987,0.55555,0.64556,76,76,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
43618,SRR6020310,SRX3171456,SRS2501265,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 hindbrain Scar,GSM2776951,,source name:hindbrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:hindbrain|sorted plates:2,R1 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:R1|tissue:hindbrain|sorted plates:2,GSM2776951,GSM2776951: R1 hindbrain Scar; Danio rerio; RNA Seq,GSM2776951,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776951,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_hindbrain_Scar_p02_R1.fastq.gz R1_hindbrain_Scar_p02_R2.fastq.gz,fastq fastq,473500697.0,3116218.0,GSM2776951 r2,0:75.99 1:75.96,A:83466014;C:138462468;G:177686415;T:73810602;N:75198,75,75,,,83466014,138462468,177686415,73810602,75198,SRX3171456,SRS2501265,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0,2e-05,0.0,0.0,1.0,0.99997,,1.0,76,75,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
43619,SRR6020307,SRX3171455,SRS2501264,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 forebrain Trans,GSM2776950,,source name:forebrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:forebrain|sorted plates:2,R1 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:R1|tissue:forebrain|sorted plates:2,GSM2776950,GSM2776950: R1 forebrain Trans; Danio rerio; RNA Seq,GSM2776950,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776950,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_forebrain_Trans_p01_R1.fastq.gz R1_forebrain_Trans_p01_R2.fastq.gz,fastq fastq,4440312865.0,29424713.0,GSM2776950 r1,0:75.40 1:75.50,A:1322530805;C:853115564;G:1047431530;T:1217034690;N:200276,75,75,,,1322530805,853115564,1047431530,1217034690,200276,SRX3171455,SRS2501264,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.07835,0.17331,0.05333,0.10793,0.96392,0.92585,0.47772,0.48547,75,75,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,Brain,Nervous System
43620,SRR6020308,SRX3171455,SRS2501264,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 forebrain Trans,GSM2776950,,source name:forebrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:forebrain|sorted plates:2,R1 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:R1|tissue:forebrain|sorted plates:2,GSM2776950,GSM2776950: R1 forebrain Trans; Danio rerio; RNA Seq,GSM2776950,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776950,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_forebrain_Trans_p02_R1.fastq.gz R1_forebrain_Trans_p02_R2.fastq.gz,fastq fastq,19165630112.0,126705173.0,GSM2776950 r2,0:75.75 1:75.51,A:4560473200;C:4803124326;G:5354362739;T:4444501864;N:3167983,75,75,,,4560473200,4803124326,5354362739,4444501864,3167983,SRX3171455,SRS2501264,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00835,0.03768,0.00561,0.02474,0.99431,0.98009,0.37028,0.42919,76,74,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
43621,SRR6020305,SRX3171454,SRS2501263,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 forebrain Scar,GSM2776949,,source name:forebrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:forebrain|sorted plates:2,R1 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:R1|tissue:forebrain|sorted plates:2,GSM2776949,GSM2776949: R1 forebrain Scar; Danio rerio; RNA Seq,GSM2776949,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_forebrain_Scar_p01_R1.fastq.gz R1_forebrain_Scar_p01_R2.fastq.gz,fastq fastq,99066891.0,652582.0,GSM2776949 r1,0:75.98 1:75.83,A:17819995;C:28634737;G:36421410;T:16186319;N:4430,75,75,,,17819995,28634737,36421410,16186319,4430,SRX3171454,SRS2501263,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00021,0.00035,0.00015,0.00024,0.99989,0.99967,0.5,0.55555,76,76,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
43622,SRR6020306,SRX3171454,SRS2501263,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 forebrain Scar,GSM2776949,,source name:forebrain single cells|cas9 injection:mRNA|FISH id:R1|tissue:forebrain|sorted plates:2,R1 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:R1|tissue:forebrain|sorted plates:2,GSM2776949,GSM2776949: R1 forebrain Scar; Danio rerio; RNA Seq,GSM2776949,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_forebrain_Scar_p02_R1.fastq.gz R1_forebrain_Scar_p02_R2.fastq.gz,fastq fastq,1051763656.0,6925286.0,GSM2776949 r2,0:75.99 1:75.89,A:187645319;C:303896142;G:395204219;T:164848985;N:168991,75,75,,,187645319,303896142,395204219,164848985,168991,SRX3171454,SRS2501263,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,4e-05,1e-05,0.0,0.99997,0.99991,0.0,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Brain,Nervous System
43625,SRR5961765,SRX3119876,SRS2454735,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 right midbrain Scars,GSM2752199,,source name:right midbrain single cells|cas9 injection:protein|FISH id:P1|tissue:right midbrain|sorted plates:1,P1 right midbrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,right 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:P1|tissue:right midbrain|sorted plates:1,GSM2752199,GSM2752199: P1 right midbrain Scars; Danio rerio; RNA Seq,GSM2752199,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752199,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_right-midbrain_p01_R1.fastq.gz P1_right-midbrain_p01_R2.fastq.gz,fastq fastq,53503999.0,352246.0,GSM2752199 r1,0:75.93 1:75.96,A:9626454;C:15363751;G:19726594;T:8769676;N:17524,75,75,,,9626454,15363751,19726594,8769676,17524,SRX3119876,SRS2454735,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00018,0.00025,0.00011,7e-05,0.99987,0.99967,0.33333,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System
43628,SRR5961763,SRX3119874,SRS2454733,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 left midbrain Scars,GSM2752197,,source name:left midbrain single cells|cas9 injection:protein|FISH id:P1|tissue:left midbrain|sorted plates:1,P1 left midbrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,left 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:P1|tissue:left midbrain|sorted plates:1,GSM2752197,GSM2752197: P1 left midbrain Scars; Danio rerio; RNA Seq,GSM2752197,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752197,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_left-midbrain_p01_R1.fastq.gz P1_left-midbrain_p01_R2.fastq.gz,fastq fastq,50471319.0,332248.0,GSM2752197 r1,0:75.97 1:75.94,A:9433855;C:14447873;G:18219586;T:8367437;N:2568,75,75,,,9433855,14447873,18219586,8367437,2568,SRX3119874,SRS2454733,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00085,0.00133,0.00068,0.00074,0.99957,0.99878,0.41935,0.55,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System
43630,SRR5961761,SRX3119872,SRS2454731,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  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 hindbrain Scars,GSM2752195,,source name:hindbrain single cells|cas9 injection:protein|FISH id:P1|tissue:hindbrain|sorted plates:2,P1 hindbrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,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:protein|FISH id:P1|tissue:hindbrain|sorted plates:2,GSM2752195,GSM2752195: P1 hindbrain Scars; Danio rerio; RNA Seq,GSM2752195,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752195,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_hindbrain_Scar_p01_R1.fastq.gz P1_hindbrain_Scar_p01_R2.fastq.gz,fastq fastq,74807718.0,492240.0,GSM2752195 r1,0:75.99 1:75.99,A:13399488;C:21374296;G:27838499;T:12190366;N:5069,75,75,,,13399488,21374296,27838499,12190366,5069,SRX3119872,SRS2454731,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,7e-05,2e-05,4e-05,0.99995,0.99993,0.33333,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System
43631,SRR6930576,SRX3119872,SRS2454731,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  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 hindbrain Scars,GSM2752195,,source name:hindbrain single cells|cas9 injection:protein|FISH id:P1|tissue:hindbrain|sorted plates:2,P1 hindbrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,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:protein|FISH id:P1|tissue:hindbrain|sorted plates:2,GSM2752195,GSM2752195: P1 hindbrain Scars; Danio rerio; RNA Seq,GSM2752195,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752195,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_hindbrain_Scar_p02_R1.fastq.gz P1_hindbrain_Scar_p02_R2.fastq.gz,fastq fastq,30414718.0,200150.0,GSM2752195 r2,0:75.98 1:75.98,A:5427121;C:8749975;G:11188832;T:5039608;N:9182,75,75,,,5427121,8749975,11188832,5039608,9182,SRX3119872,SRS2454731,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00016,6e-05,8e-05,3e-05,0.99991,0.99993,0.15384,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System
43632,SRR5961760,SRX3119871,SRS2454730,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  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 forebrain Scars,GSM2752194,,source name:forebrain single cells|cas9 injection:protein|FISH id:P1|tissue:forebrain|sorted plates:2,P1 forebrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,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:P1|tissue:forebrain|sorted plates:2,GSM2752194,GSM2752194: P1 forebrain Scars; Danio rerio; RNA Seq,GSM2752194,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752194,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_forebrain_Scar_p01_R1.fastq.gz P1_forebrain_Scar_p01_R2.fastq.gz,fastq fastq,111111360.0,731095.0,GSM2752194 r1,0:75.99 1:75.99,A:20001359;C:32539820;G:41186423;T:17376363;N:7395,75,75,,,20001359,32539820,41186423,17376363,7395,SRX3119871,SRS2454730,SRA602108,GEO,"AVO, Hubrecht Institue",2,2e-05,2e-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,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System
43633,SRR6930575,SRX3119871,SRS2454730,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  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 forebrain Scars,GSM2752194,,source name:forebrain single cells|cas9 injection:protein|FISH id:P1|tissue:forebrain|sorted plates:2,P1 forebrain Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,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:P1|tissue:forebrain|sorted plates:2,GSM2752194,GSM2752194: P1 forebrain Scars; Danio rerio; RNA Seq,GSM2752194,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752194,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_forebrain_Scar_p02_R1.fastq.gz P1_forebrain_Scar_p02_R2.fastq.gz,fastq fastq,18261190.0,120170.0,GSM2752194 r2,0:75.98 1:75.98,A:3279493;C:5448202;G:6687629;T:2839767;N:6099,75,75,,,3279493,5448202,6687629,2839767,6099,SRX3119871,SRS2454730,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00021,0.00028,0.00018,0.00019,0.99997,0.99983,0.0,0.44444,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Brain,Nervous System