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
43499,SRR6020425,SRX3171489,SRS2501298,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Trans,GSM2776984,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776984,GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq,GSM2776984,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Trans_p01_R1.fastq.gz R4_wkm_Trans_p01_R2.fastq.gz,fastq fastq,3927170013.0,26023917.0,GSM2776984 r1,0:75.41 1:75.50,A:1129996659;C:572501533;G:611837437;T:1612813099;N:21285,75,75,,,1129996659,572501533,611837437,1612813099,21285,SRX3171489,SRS2501298,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.32239,0.87342,0.20343,0.36809,0.95722,0.82919,0.49895,0.48491,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43500,SRR6020426,SRX3171489,SRS2501298,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Trans,GSM2776984,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776984,GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq,GSM2776984,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Trans_p02_R1.fastq.gz R4_wkm_Trans_p02_R2.fastq.gz,fastq fastq,4030497815.0,26709253.0,GSM2776984 r2,0:75.41 1:75.49,A:1162066088;C:581519292;G:627111524;T:1659778815;N:22096,75,75,,,1162066088,581519292,627111524,1659778815,22096,SRX3171489,SRS2501298,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33073,0.87349,0.21896,0.35721,0.96337,0.82895,0.48607,0.49848,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43501,SRR6020427,SRX3171489,SRS2501298,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Trans,GSM2776984,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776984,GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq,GSM2776984,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Trans_p03_R1.fastq.gz R4_wkm_Trans_p03_R2.fastq.gz,fastq fastq,3631053942.0,24060145.0,GSM2776984 r3,0:75.46 1:75.46,A:1043256309;C:532046798;G:537476503;T:1518171924;N:102408,75,75,,,1043256309,532046798,537476503,1518171924,102408,SRX3171489,SRS2501298,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.32814,0.80344,0.24082,0.39956,0.96319,0.85831,0.49813,0.5276,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43502,SRR6020428,SRX3171489,SRS2501298,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Trans,GSM2776984,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776984,GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq,GSM2776984,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Trans_p04_R1.fastq.gz R4_wkm_Trans_p04_R2.fastq.gz,fastq fastq,4828053523.0,31991602.0,GSM2776984 r4,0:75.42 1:75.50,A:1401132307;C:703203743;G:750174359;T:1973515875;N:27239,75,75,,,1401132307,703203743,750174359,1973515875,27239,SRX3171489,SRS2501298,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.3505,0.86169,0.26499,0.42336,0.96027,0.8182,0.49142,0.49842,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43503,SRR6020421,SRX3171488,SRS2501297,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Scar,GSM2776983,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776983,GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq,GSM2776983,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Scar_p01_R1.fastq.gz R4_wkm_Scar_p01_R2.fastq.gz,fastq fastq,614245655.0,4041684.0,GSM2776983 r1,0:75.99 1:75.99,A:107048177;C:178914249;G:231725646;T:96554319;N:3264,75,75,,,107048177,178914249,231725646,96554319,3264,SRX3171488,SRS2501297,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,0.00013,1e-05,8e-05,0.99997,0.99991,1.0,0.875,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43504,SRR6020422,SRX3171488,SRS2501297,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Scar,GSM2776983,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776983,GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq,GSM2776983,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Scar_p02_R1.fastq.gz R4_wkm_Scar_p02_R2.fastq.gz,fastq fastq,817459087.0,5378786.0,GSM2776983 r2,0:75.99 1:75.99,A:143806910;C:238933705;G:307736025;T:126978347;N:4100,75,75,,,143806910,238933705,307736025,126978347,4100,SRX3171488,SRS2501297,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,4e-05,1e-05,1e-05,0.99995,0.99995,0.5,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43505,SRR6020423,SRX3171488,SRS2501297,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Scar,GSM2776983,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776983,GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq,GSM2776983,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Scar_p03_R1.fastq.gz R4_wkm_Scar_p03_R2.fastq.gz,fastq fastq,3981890019.0,26204072.0,GSM2776983 r3,0:75.98 1:75.97,A:703462533;C:1148861227;G:1510546877;T:618921234;N:98148,75,75,,,703462533,1148861227,1510546877,618921234,98148,SRX3171488,SRS2501297,SRA602108,GEO,"AVO, Hubrecht Institue",2,7e-05,9e-05,4e-05,4e-05,0.99993,0.99987,0.25,0.42857,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43506,SRR6020424,SRX3171488,SRS2501297,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 wkm Scar,GSM2776983,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,R4 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4,GSM2776983,GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq,GSM2776983,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_wkm_Scar_p04_R1.fastq.gz R4_wkm_Scar_p04_R2.fastq.gz,fastq fastq,561112602.0,3692109.0,GSM2776983 r4,0:75.98 1:75.99,A:98682129;C:162936789;G:209922290;T:89568564;N:2830,75,75,,,98682129,162936789,209922290,89568564,2830,SRX3171488,SRS2501297,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00016,9e-05,4e-05,5e-05,0.99973,0.99993,0.72727,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43565,SRR6020354,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p01_R2.fastq.gz R2_wkm_Trans_p01_R1.fastq.gz,fastq fastq,9024550362.0,59819416.0,GSM2776964 r1,0:75.43 1:75.43,A:2680475382;C:1320224241;G:1470728320;T:3553005800;N:116619,75,75,,,2680475382,1320224241,1470728320,3553005800,116619,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.3361,0.6658,0.26022,0.30025,0.9655,0.84861,0.54877,0.53502,73,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43566,SRR6020355,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p02_R1.fastq.gz R2_wkm_Trans_p02_R2.fastq.gz,fastq fastq,6846456986.0,45296050.0,GSM2776964 r2,0:75.58 1:75.57,A:1794290868;C:1266097894;G:1480877558;T:2305103809;N:86857,75,75,,,1794290868,1266097894,1480877558,2305103809,86857,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.12369,0.58191,0.08122,0.21507,0.96917,0.86478,0.54436,0.52833,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43567,SRR6020356,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p04_R1.fastq.gz R2_wkm_Trans_p04_R2.fastq.gz,fastq fastq,6833024281.0,45038138.0,GSM2776964 r3,0:75.92 1:75.80,A:1377999605;C:1844050318;G:2309866401;T:1300399227;N:708730,75,75,,,1377999605,1844050318,2309866401,1300399227,708730,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01228,0.03967,0.01047,0.02854,0.996,0.98784,0.46886,0.40014,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43568,SRR6020357,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p05_R1.fastq.gz R2_wkm_Trans_p05_R2.fastq.gz,fastq fastq,10064318519.0,66330889.0,GSM2776964 r4,0:75.93 1:75.80,A:2012776438;C:2737247628;G:3409080553;T:1904157367;N:1056533,75,75,,,2012776438,2737247628,3409080553,1904157367,1056533,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01861,0.04126,0.01632,0.03024,0.99537,0.9852,0.46531,0.52808,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43569,SRR6020358,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p06_R1.fastq.gz R2_wkm_Trans_p06_R2.fastq.gz,fastq fastq,6687331360.0,44108617.0,GSM2776964 r5,0:75.86 1:75.75,A:1437098890;C:1744557843;G:2166182975;T:1338781574;N:710078,75,75,,,1437098890,1744557843,2166182975,1338781574,710078,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.02427,0.05957,0.02134,0.04215,0.99504,0.98561,0.59024,0.56702,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43570,SRR6020359,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p07_R1.fastq.gz R2_wkm_Trans_p07_R2.fastq.gz,fastq fastq,5153832004.0,34073366.0,GSM2776964 r6,0:75.66 1:75.60,A:1326888770;C:1102939496;G:1274553839;T:1448364985;N:1084914,75,75,,,1326888770,1102939496,1274553839,1448364985,1084914,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.1589,0.37012,0.13594,0.2937,0.96008,0.89796,0.53952,0.50866,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43571,SRR6020360,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p08_R1.fastq.gz R2_wkm_Trans_p08_R2.fastq.gz,fastq fastq,6115949904.0,40453679.0,GSM2776964 r7,0:75.63 1:75.55,A:1597313172;C:1289666072;G:1493416158;T:1734258580;N:1295922,75,75,,,1597313172,1289666072,1493416158,1734258580,1295922,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.13807,0.341,0.11368,0.25445,0.96546,0.90859,0.52718,0.49692,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43572,SRR6020361,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p09_R1.fastq.gz R2_wkm_Trans_p09_R2.fastq.gz,fastq fastq,5237730043.0,34642054.0,GSM2776964 r8,0:75.63 1:75.57,A:1366106800;C:1100303416;G:1291870046;T:1478328279;N:1121502,75,75,,,1366106800,1100303416,1291870046,1478328279,1121502,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.12743,0.30857,0.10066,0.19993,0.96899,0.91999,0.50164,0.55176,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43573,SRR6020362,SRX3171469,SRS2501278,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Trans,GSM2776964,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776964,GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq,GSM2776964,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Trans_p10_R2.fastq.gz R2_wkm_Trans_p10_R1.fastq.gz,fastq fastq,5966158980.0,39481315.0,GSM2776964 r9,0:75.59 1:75.53,A:1608448002;C:1182029002;G:1349064196;T:1825357615;N:1260165,75,75,,,1608448002,1182029002,1349064196,1825357615,1260165,SRX3171469,SRS2501278,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.14278,0.40505,0.11298,0.25782,0.96169,0.88933,0.53335,0.51935,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43574,SRR6020345,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p01_R1.fastq.gz R2_wkm_Scar_p01_R2.fastq.gz,fastq fastq,1684853042.0,11092789.0,GSM2776963 r1,0:75.97 1:75.92,A:295001511;C:489169550;G:629447507;T:271215194;N:19280,75,75,,,295001511,489169550,629447507,271215194,19280,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00026,0.00111,0.00021,0.00081,0.99983,0.99931,0.625,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43575,SRR6020346,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p02_R1.fastq.gz R2_wkm_Scar_p02_R2.fastq.gz,fastq fastq,2167767595.0,14269042.0,GSM2776963 r2,0:75.97 1:75.95,A:393119574;C:622441995;G:803855479;T:348326899;N:23648,75,75,,,393119574,622441995,803855479,348326899,23648,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,4e-05,0.00012,2e-05,0.99997,0.99997,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43576,SRR6020347,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p04_R1.fastq.gz R2_wkm_Scar_p04_R2.fastq.gz,fastq fastq,949039352.0,6246899.0,GSM2776963 r3,0:75.98 1:75.94,A:168664399;C:275210713;G:354697026;T:150353667;N:113547,75,75,,,168664399,275210713,354697026,150353667,113547,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,1e-05,4e-05,0.0,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43577,SRR6020348,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p05_R1.fastq.gz R2_wkm_Scar_p05_R2.fastq.gz,fastq fastq,708086378.0,4660800.0,GSM2776963 r4,0:75.98 1:75.94,A:125487931;C:204868898;G:265817122;T:111841010;N:71417,75,75,,,125487931,204868898,265817122,111841010,71417,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,0.0,3e-05,0.0,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43578,SRR6020349,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p06_R1.fastq.gz R2_wkm_Scar_p06_R2.fastq.gz,fastq fastq,1334977556.0,8786739.0,GSM2776963 r5,0:75.98 1:75.95,A:236705935;C:386768904;G:500728970;T:210637790;N:135957,75,75,,,236705935,386768904,500728970,210637790,135957,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,2e-05,0.0,1e-05,0.0,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43579,SRR6020350,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p07_R1.fastq.gz R2_wkm_Scar_p07_R2.fastq.gz,fastq fastq,560151517.0,3686527.0,GSM2776963 r6,0:75.99 1:75.96,A:99216542;C:162559282;G:209970335;T:88295033;N:110325,75,75,,,99216542,162559282,209970335,88295033,110325,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00013,0.00031,0.0001,0.00024,0.99989,0.99977,0.4,0.18181,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43580,SRR6020351,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p08_R1.fastq.gz R2_wkm_Scar_p08_R2.fastq.gz,fastq fastq,581077562.0,3824465.0,GSM2776963 r7,0:75.98 1:75.95,A:103035022;C:167783256;G:218182356;T:91955266;N:121662,75,75,,,103035022,167783256,218182356,91955266,121662,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00012,0.00017,0.0001,0.0001,0.99995,0.99983,0.33333,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43581,SRR6020352,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p09_R1.fastq.gz R2_wkm_Scar_p09_R2.fastq.gz,fastq fastq,540845179.0,3559589.0,GSM2776963 r8,0:75.98 1:75.96,A:95821696;C:156515054;G:202433894;T:85962271;N:112264,75,75,,,95821696,156515054,202433894,85962271,112264,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00022,0.00026,0.00017,0.00017,0.99985,0.99975,0.42857,0.61538,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43582,SRR6020353,SRX3171468,SRS2501277,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R2 wkm Scar,GSM2776963,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,R2 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9,GSM2776963,GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq,GSM2776963,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R2_wkm_Scar_p10_R1.fastq.gz R2_wkm_Scar_p10_R2.fastq.gz,fastq fastq,839350049.0,5524195.0,GSM2776963 r9,0:75.98 1:75.96,A:148919223;C:243407956;G:314166938;T:132682976;N:172956,75,75,,,148919223,243407956,314166938,132682976,172956,SRX3171468,SRS2501277,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00026,0.00065,0.00022,0.00044,0.99987,0.99935,0.5,0.69696,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43583,SRR6020335,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p01_R1.fastq.gz R1_wkm_Trans_p01_R2.fastq.gz,fastq fastq,5973924896.0,39414942.0,GSM2776962 r1,0:75.90 1:75.67,A:1246713886;C:1600299713;G:1930846373;T:1194812009;N:1252915,75,75,,,1246713886,1600299713,1930846373,1194812009,1252915,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01167,0.032,0.00909,0.02214,0.99644,0.98829,0.31168,0.44038,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43584,SRR6020336,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p10_R1.fastq.gz R1_wkm_Trans_p10_R2.fastq.gz,fastq fastq,2617289615.0,17271557.0,GSM2776962 r10,0:75.82 1:75.72,A:567948720;C:650310169;G:793147028;T:605454241;N:429457,75,75,,,567948720,650310169,793147028,605454241,429457,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0644,0.15708,0.05669,0.13057,0.98198,0.94714,0.50177,0.51068,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43585,SRR6020337,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p02_R1.fastq.gz R1_wkm_Trans_p02_R2.fastq.gz,fastq fastq,7594280551.0,50128244.0,GSM2776962 r2,0:75.86 1:75.63,A:1634649789;C:1975593425;G:2355482941;T:1626855827;N:1698569,75,75,,,1634649789,1975593425,2355482941,1626855827,1698569,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01418,0.05132,0.01052,0.03283,0.99411,0.98096,0.42315,0.47699,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43586,SRR6020338,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p03_R1.fastq.gz R1_wkm_Trans_p03_R2.fastq.gz,fastq fastq,10033302083.0,66227671.0,GSM2776962 r3,0:75.87 1:75.63,A:2174708635;C:2640912986;G:3104545578;T:2110890445;N:2244439,75,75,,,2174708635,2640912986,3104545578,2110890445,2244439,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01909,0.05761,0.01497,0.0388,0.99527,0.98559,0.62157,0.383,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43587,SRR6020339,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p04_R1.fastq.gz R1_wkm_Trans_p04_R2.fastq.gz,fastq fastq,6711074817.0,44294742.0,GSM2776962 r4,0:75.86 1:75.65,A:1427276784;C:1758105877;G:2110503657;T:1413707482;N:1481017,75,75,,,1427276784,1758105877,2110503657,1413707482,1481017,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01603,0.04728,0.01155,0.02826,0.99537,0.98275,0.40869,0.46908,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43588,SRR6020340,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p05_R1.fastq.gz R1_wkm_Trans_p05_R2.fastq.gz,fastq fastq,5218937446.0,34471555.0,GSM2776962 r5,0:75.81 1:75.59,A:1215811466;C:1256980753;G:1501056299;T:1243910449;N:1178479,75,75,,,1215811466,1256980753,1501056299,1243910449,1178479,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.02337,0.08686,0.0188,0.05946,0.99561,0.98139,0.29979,0.497,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43589,SRR6020341,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p06_R1.fastq.gz R1_wkm_Trans_p06_R2.fastq.gz,fastq fastq,6108807000.0,40436337.0,GSM2776962 r6,0:75.61 1:75.47,A:1673719828;C:1137235460;G:1275308369;T:2021133061;N:1410282,75,75,,,1673719828,1137235460,1275308369,2021133061,1410282,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.10437,0.31204,0.0749,0.16508,0.97881,0.92991,0.45043,0.51006,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43590,SRR6020342,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p07_R1.fastq.gz R1_wkm_Trans_p07_R2.fastq.gz,fastq fastq,4731732871.0,31235538.0,GSM2776962 r7,0:75.80 1:75.69,A:1076749811;C:1116149409;G:1331817067;T:1206252219;N:764365,75,75,,,1076749811,1116149409,1331817067,1206252219,764365,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.06387,0.1773,0.05441,0.13368,0.98293,0.93825,0.51607,0.52472,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43591,SRR6020343,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p08_R1.fastq.gz R1_wkm_Trans_p08_R2.fastq.gz,fastq fastq,4880262283.0,32178172.0,GSM2776962 r8,0:75.90 1:75.76,A:984048995;C:1311633495;G:1623325534;T:960451784;N:802475,75,75,,,984048995,1311633495,1623325534,960451784,802475,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01625,0.04758,0.01254,0.03334,0.99119,0.97512,0.51741,0.48393,75,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43592,SRR6020344,SRX3171467,SRS2501276,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Trans,GSM2776962,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776962,GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq,GSM2776962,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Trans_p09_R1.fastq.gz R1_wkm_Trans_p09_R2.fastq.gz,fastq fastq,2281506515.0,15040814.0,GSM2776962 r9,0:75.91 1:75.78,A:455027935;C:614063661;G:762091600;T:449957278;N:366041,75,75,,,455027935,614063661,762091600,449957278,366041,SRX3171467,SRS2501276,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.02501,0.0603,0.022,0.04691,0.99159,0.97228,0.50712,0.52872,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43593,SRR6020325,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p01_R1.fastq.gz R1_wkm_Scar_p01_R2.fastq.gz,fastq fastq,1160781646.0,7644126.0,GSM2776961 r1,0:75.98 1:75.87,A:206133465;C:337727978;G:433057561;T:183619190;N:243452,75,75,,,206133465,337727978,433057561,183619190,243452,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,1e-05,0.0,0.0,0.0,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43594,SRR6020326,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p10_R1.fastq.gz R1_wkm_Scar_p10_R2.fastq.gz,fastq fastq,444321370.0,2925523.0,GSM2776961 r10,0:75.98 1:75.89,A:78895877;C:128614562;G:165020269;T:71718452;N:72210,75,75,,,78895877,128614562,165020269,71718452,72210,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00013,0.00022,8e-05,0.0001,0.99995,0.99969,0.0,0.4375,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43595,SRR6020327,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p02_R1.fastq.gz R1_wkm_Scar_p02_R2.fastq.gz,fastq fastq,1118531897.0,7366750.0,GSM2776961 r2,0:75.98 1:75.85,A:199272195;C:323746349;G:416605188;T:178669664;N:238501,75,75,,,199272195,323746349,416605188,178669664,238501,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,2e-05,9e-05,0.0,2e-05,0.99997,0.99987,1.0,0.28571,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43596,SRR6020328,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p03_R1.fastq.gz R1_wkm_Scar_p03_R2.fastq.gz,fastq fastq,842900122.0,5552138.0,GSM2776961 r3,0:75.98 1:75.83,A:149698513;C:244376973;G:313988330;T:134655045;N:181261,75,75,,,149698513,244376973,313988330,134655045,181261,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,9e-05,2e-05,4e-05,0.99993,0.99989,0.66666,0.8,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43597,SRR6020329,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p04_R1.fastq.gz R1_wkm_Scar_p04_R2.fastq.gz,fastq fastq,983580857.0,6477811.0,GSM2776961 r4,0:75.98 1:75.86,A:173458414;C:285222602;G:367968109;T:156722927;N:208805,75,75,,,173458414,285222602,367968109,156722927,208805,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,1e-05,0.0,0.0,0.0,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43598,SRR6020330,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p05_R1.fastq.gz R1_wkm_Scar_p05_R2.fastq.gz,fastq fastq,542048001.0,3570304.0,GSM2776961 r5,0:75.98 1:75.84,A:96887298;C:156549850;G:201875058;T:86619073;N:116722,75,75,,,96887298,156549850,201875058,86619073,116722,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,1e-05,3e-05,0.0,0.99997,0.99997,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43599,SRR6020331,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p06_R1.fastq.gz R1_wkm_Scar_p06_R2.fastq.gz,fastq fastq,1331503316.0,8770302.0,GSM2776961 r6,0:75.98 1:75.84,A:239821115;C:383865311;G:491153102;T:216395981;N:267807,75,75,,,239821115,383865311,491153102,216395981,267807,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00035,0.00029,0.00023,0.00015,0.99989,0.99973,0.125,0.46153,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43600,SRR6020332,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p07_R1.fastq.gz R1_wkm_Scar_p07_R2.fastq.gz,fastq fastq,443058723.0,2917225.0,GSM2776961 r7,0:75.99 1:75.89,A:78132383;C:128408112;G:164997328;T:71447465;N:73435,75,75,,,78132383,128408112,164997328,71447465,73435,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00011,0.00017,8e-05,0.00014,0.99993,0.99991,0.25,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43601,SRR6020333,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p08_R1.fastq.gz R1_wkm_Scar_p08_R2.fastq.gz,fastq fastq,460136778.0,3029705.0,GSM2776961 r8,0:75.99 1:75.89,A:81219078;C:133929839;G:170892657;T:74024644;N:70560,75,75,,,81219078,133929839,170892657,74024644,70560,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,2e-05,2e-05,1e-05,0.0,0.99997,0.99997,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43602,SRR6020334,SRX3171466,SRS2501275,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R1 wkm Scar,GSM2776961,,source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,R1 wkm Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10,GSM2776961,GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq,GSM2776961,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R1_wkm_Scar_p09_R1.fastq.gz R1_wkm_Scar_p09_R2.fastq.gz,fastq fastq,495182451.0,3261129.0,GSM2776961 r9,0:75.98 1:75.87,A:89479589;C:142929535;G:181791653;T:80902228;N:79446,75,75,,,89479589,142929535,181791653,80902228,79446,SRX3171466,SRS2501275,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00037,0.00149,0.00026,0.00096,0.99969,0.99855,0.22222,0.3647,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Kidney,Renal System
43634,SRR5961758,SRX3119870,SRS2454729,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 wkm Scars,GSM2752193,,source name:wkm single cells|cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2,P1 wkm Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2,GSM2752193,GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq,GSM2752193,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752193,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_wkm_Scar_p01_R1.fastq.gz P1_wkm_Scar_p01_R2.fastq.gz,fastq fastq,995569951.0,6550623.0,GSM2752193 r1,0:75.99 1:75.99,A:179447412;C:292592664;G:370193004;T:153293464;N:43407,75,75,,,179447412,292592664,370193004,153293464,43407,SRX3119870,SRS2454729,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,4e-05,0.00013,3e-05,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Kidney,Renal System
43635,SRR5961759,SRX3119870,SRS2454729,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 wkm Scars,GSM2752193,,source name:wkm single cells|cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2,P1 wkm Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,wkm single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2,GSM2752193,GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq,GSM2752193,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752193,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_wkm_Scar_p02_R1.fastq.gz P1_wkm_Scar_p02_R2.fastq.gz,fastq fastq,941664617.0,6196187.0,GSM2752193 r2,0:75.99 1:75.99,A:170094338;C:275555653;G:348702043;T:147269855;N:42728,75,75,,,170094338,275555653,348702043,147269855,42728,SRX3119870,SRS2454729,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00033,0.0001,0.00027,8e-05,0.99987,0.99993,0.625,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Kidney,Renal System