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
43472,SRR6888831,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-003-Scar_R1.fastq.gz P2-CFin-Vent-003-Scar_R2.fastq.gz,fastq fastq,344793287.0,2269321.0,GSM3065988 r1,0:75.99 1:75.95,A:61565924;C:101344805;G:127059615;T:54785853;N:37090,75,75,,,61565924,101344805,127059615,54785853,37090,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,0.00029,0.00012,0.00017,0.99993,0.99977,0.33333,0.58823,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43473,SRR6888832,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz,fastq fastq,110701966.0,728490.0,GSM3065988 r2,0:75.99 1:75.97,A:19507928;C:32552811;G:40930271;T:17699467;N:11489,75,75,,,19507928,32552811,40930271,17699467,11489,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00021,0.0004,0.00015,0.00031,0.99991,0.99981,1.0,0.84615,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43474,SRR6888829,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-003-Scar_R2.fastq.gz P2-CFin-Dors-003-Scar_R1.fastq.gz,fastq fastq,537943644.0,3539989.0,GSM3065987 r1,0:75.99 1:75.97,A:94708808;C:157878001;G:198461680;T:86838061;N:57094,75,75,,,94708808,157878001,198461680,86838061,57094,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00016,0.00102,0.0001,0.00067,0.99995,0.99995,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43475,SRR6888830,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz,fastq fastq,856597590.0,5637115.0,GSM3065987 r2,0:75.99 1:75.97,A:151359975;C:251587454;G:317011744;T:136549208;N:89209,75,75,,,151359975,251587454,317011744,136549208,89209,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00027,0.00065,0.00016,0.00039,0.99975,0.99951,0.29411,0.53658,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43476,SRR6020446,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p01_R1.fastq.gz R5_sec_Trans_p01_R2.fastq.gz,fastq fastq,5031589058.0,33202740.0,GSM2776988 r1,0:75.79 1:75.75,A:1144328847;C:1211156155;G:1480041764;T:1195826451;N:235841,75,75,,,1144328847,1211156155,1480041764,1195826451,235841,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.11853,0.24563,0.10636,0.21925,0.96585,0.92555,0.49894,0.48592,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43477,SRR6020447,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p02_R2.fastq.gz R5_sec_Trans_p02_R1.fastq.gz,fastq fastq,5020749563.0,33189212.0,GSM2776988 r2,0:75.66 1:75.61,A:1271180542;C:1081665590;G:1257183505;T:1410487545;N:232381,75,75,,,1271180542,1081665590,1257183505,1410487545,232381,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.12477,0.33055,0.10671,0.26254,0.96773,0.90583,0.50071,0.48529,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43478,SRR6020448,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p03_R1.fastq.gz R5_sec_Trans_p03_R2.fastq.gz,fastq fastq,9930849737.0,65769125.0,GSM2776988 r3,0:75.49 1:75.50,A:2771601461;C:1594447174;G:1778419273;T:3786066213;N:315616,75,75,,,2771601461,1594447174,1778419273,3786066213,315616,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.31895,0.74881,0.28344,0.57326,0.96546,0.85234,0.4987,0.52017,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43479,SRR6020449,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p04_R1.fastq.gz R5_sec_Trans_p04_R2.fastq.gz,fastq fastq,7297925579.0,48343134.0,GSM2776988 r4,0:75.51 1:75.45,A:2157432534;C:1129186071;G:1200823243;T:2810444585;N:39146,75,75,,,2157432534,1129186071,1200823243,2810444585,39146,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.352,0.75293,0.31357,0.60441,0.95828,0.83885,0.50134,0.50535,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43480,SRR6020450,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p05_R2.fastq.gz R5_sec_Trans_p05_R1.fastq.gz,fastq fastq,13855953318.0,91804628.0,GSM2776988 r5,0:75.50 1:75.43,A:4146316683;C:2217362039;G:2391706547;T:5100492721;N:75328,75,75,,,4146316683,2217362039,2391706547,5100492721,75328,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.37449,0.68646,0.32985,0.54102,0.95347,0.849,0.49416,0.50708,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43481,SRR6020451,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p06_R1.fastq.gz R5_sec_Trans_p06_R2.fastq.gz,fastq fastq,9723577592.0,64415623.0,GSM2776988 r6,0:75.50 1:75.45,A:2835431401;C:1511580093;G:1616039076;T:3760473139;N:53883,75,75,,,2835431401,1511580093,1616039076,3760473139,53883,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33655,0.77492,0.29229,0.58155,0.95978,0.8454,0.49546,0.51051,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43482,SRR6020440,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p01_R1.fastq.gz R5_sec_Scar_p01_R2.fastq.gz,fastq fastq,361194076.0,2376599.0,GSM2776987 r1,0:75.99 1:75.99,A:63932353;C:105212754;G:137339472;T:54692604;N:16893,75,75,,,63932353,105212754,137339472,54692604,16893,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,7e-05,0.00012,4e-05,9e-05,0.99993,0.99991,0.5,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43483,SRR6020441,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p02_R1.fastq.gz R5_sec_Scar_p02_R2.fastq.gz,fastq fastq,460055993.0,3027108.0,GSM2776987 r2,0:75.99 1:75.99,A:80579341;C:134185300;G:175364991;T:69904520;N:21841,75,75,,,80579341,134185300,175364991,69904520,21841,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,2e-05,2e-05,0.0,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43484,SRR6020442,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p03_R1.fastq.gz R5_sec_Scar_p03_R2.fastq.gz,fastq fastq,466000423.0,3066554.0,GSM2776987 r3,0:75.98 1:75.98,A:81301391;C:136221817;G:177874701;T:70591092;N:11422,75,75,,,81301391,136221817,177874701,70591092,11422,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0001,0.00016,8e-05,0.00011,0.99993,0.99987,0.0,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43485,SRR6020443,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p04_R1.fastq.gz R5_sec_Scar_p04_R2.fastq.gz,fastq fastq,203843839.0,1341388.0,GSM2776987 r4,,,,,,,,,,,,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00013,0.00027,9e-05,0.00019,0.99995,0.99977,0.16666,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43486,SRR6020444,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p05_R1.fastq.gz R5_sec_Scar_p05_R2.fastq.gz,fastq fastq,305866297.0,2012742.0,GSM2776987 r5,0:75.98 1:75.98,A:53459692;C:89448285;G:116312720;T:46644195;N:1405,75,75,,,53459692,89448285,116312720,46644195,1405,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,6e-05,9e-05,3e-05,5e-05,0.99997,0.99993,0.0,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43487,SRR6020445,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p06_R1.fastq.gz R5_sec_Scar_p06_R2.fastq.gz,fastq fastq,557494800.0,3670391.0,GSM2776987 r6,0:75.96 1:75.93,A:101252524;C:160223186;G:205832526;T:90183664;N:2900,75,75,,,101252524,160223186,205832526,90183664,2900,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00382,0.00768,0.00317,0.00636,0.99827,0.99673,0.48648,0.5,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43488,SRR6020435,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p02_R1.fastq.gz R5_prim_Trans_p02_R2.fastq.gz,fastq fastq,7812360278.0,51697480.0,GSM2776986 r1,0:75.54 1:75.58,A:2098454376;C:1641311761;G:1943503636;T:2128270555;N:819950,75,75,,,2098454376,1641311761,1943503636,2128270555,819950,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.01048,0.02593,0.00847,0.02007,0.99614,0.98742,0.33227,0.53419,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43489,SRR6020436,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p03_R1.fastq.gz R5_prim_Trans_p03_R2.fastq.gz,fastq fastq,6704494628.0,44436630.0,GSM2776986 r2,0:75.49 1:75.39,A:2087008571;C:1124579474;G:1252171872;T:2240541544;N:193167,75,75,,,2087008571,1124579474,1252171872,2240541544,193167,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.24966,0.47946,0.21997,0.40259,0.95162,0.89191,0.48641,0.54514,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43490,SRR6020437,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p04_R1.fastq.gz R5_prim_Trans_p04_R2.fastq.gz,fastq fastq,8402262674.0,55692887.0,GSM2776986 r3,0:75.48 1:75.39,A:2618499207;C:1444061167;G:1613776766;T:2725680678;N:244856,75,75,,,2618499207,1444061167,1613776766,2725680678,244856,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.26079,0.43317,0.23304,0.36897,0.95686,0.90575,0.50825,0.53432,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43491,SRR6020438,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p07_R1.fastq.gz R5_prim_Trans_p07_R2.fastq.gz,fastq fastq,7045442122.0,46667895.0,GSM2776986 r4,0:75.65 1:75.32,A:1992737539;C:1481998828;G:1584855122;T:1984679859;N:1170774,75,75,,,1992737539,1481998828,1584855122,1984679859,1170774,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.08866,0.20939,0.07714,0.18048,0.97906,0.95674,0.50746,0.52807,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43492,SRR6020439,SRX3171491,SRS2501300,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Trans,GSM2776986,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,R5 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:5,GSM2776986,GSM2776986: R5 prim Trans; Danio rerio; RNA Seq,GSM2776986,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Trans_p08_R1.fastq.gz R5_prim_Trans_p08_R2.fastq.gz,fastq fastq,18530449971.0,122665653.0,GSM2776986 r5,0:75.68 1:75.38,A:4667348302;C:4333487274;G:4681098112;T:4848415162;N:101121,75,75,,,4667348302,4333487274,4681098112,4848415162,101121,SRX3171491,SRS2501300,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.05599,0.12252,0.04627,0.10255,0.98409,0.96467,0.50898,0.5274,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43493,SRR6020429,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p01_R1.fastq.gz R5_prim_Scar_p01_R2.fastq.gz,fastq fastq,24766319.0,163126.0,GSM2776985 r1,0:75.95 1:75.87,A:4693411;C:6959422;G:8727578;T:4381992;N:3916,75,75,,,4693411,6959422,8727578,4381992,3916,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00023,0.00064,0.00018,0.00044,0.99989,0.99969,0.6,0.8,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43494,SRR6020430,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p02_R1.fastq.gz R5_prim_Scar_p02_R2.fastq.gz,fastq fastq,1266120923.0,8332017.0,GSM2776985 r2,0:75.98 1:75.98,A:222649072;C:369728088;G:482809574;T:190903334;N:30855,75,75,,,222649072,369728088,482809574,190903334,30855,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,2e-05,3e-05,1e-05,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43495,SRR6020431,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p03_R1.fastq.gz R5_prim_Scar_p03_R2.fastq.gz,fastq fastq,494949145.0,3257351.0,GSM2776985 r3,0:75.98 1:75.97,A:87163836;C:143707892;G:188542837;T:75522642;N:11938,75,75,,,87163836,143707892,188542837,75522642,11938,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,5e-05,9e-05,2e-05,0.99995,0.99993,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43496,SRR6020432,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p04_R1.fastq.gz R5_prim_Scar_p04_R2.fastq.gz,fastq fastq,376701290.0,2478856.0,GSM2776985 r4,0:75.99 1:75.98,A:66002492;C:109979363;G:143811826;T:56905698;N:1911,75,75,,,66002492,109979363,143811826,56905698,1911,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,5e-05,3e-05,4e-05,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43497,SRR6020433,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p07_R1.fastq.gz R5_prim_Scar_p07_R2.fastq.gz,fastq fastq,34956996.0,230152.0,GSM2776985 r5,0:75.96 1:75.92,A:6443422;C:10072498;G:12853211;T:5583477;N:4388,75,75,,,6443422,10072498,12853211,5583477,4388,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00459,0.01152,0.00401,0.00964,0.99821,0.99624,0.43333,0.53588,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43498,SRR6020434,SRX3171490,SRS2501299,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 prim Scar,GSM2776985,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,R5 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:primary fin|sorted plates:6,GSM2776985,GSM2776985: R5 prim Scar; Danio rerio; RNA Seq,GSM2776985,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_prim_Scar_p08_R1.fastq.gz R5_prim_Scar_p08_R2.fastq.gz,fastq fastq,833299107.0,5483661.0,GSM2776985 r6,0:75.98 1:75.98,A:145414972;C:243570136;G:319061924;T:125238697;N:13378,75,75,,,145414972,243570136,319061924,125238697,13378,SRX3171490,SRS2501299,SRA602108,GEO,"AVO, Hubrecht Institue",2,6e-05,8e-05,2e-05,3e-05,0.99991,0.99989,0.75,0.8,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43507,SRR6020417,SRX3171487,SRS2501295,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Trans,GSM2776982,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776982,GSM2776982: R4 terv Trans; Danio rerio; RNA Seq,GSM2776982,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Trans_p01_R1.fastq.gz R4_terv_Trans_p01_R2.fastq.gz,fastq fastq,899878376.0,5966262.0,GSM2776982 r1,0:75.45 1:75.38,A:292042567;C:146271033;G:139925382;T:321623997;N:15397,75,75,,,292042567,146271033,139925382,321623997,15397,SRX3171487,SRS2501295,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33677,0.59727,0.29432,0.51752,0.95641,0.92176,0.48959,0.52071,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43508,SRR6020418,SRX3171487,SRS2501295,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Trans,GSM2776982,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776982,GSM2776982: R4 terv Trans; Danio rerio; RNA Seq,GSM2776982,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Trans_p02_R2.fastq.gz R4_terv_Trans_p02_R1.fastq.gz,fastq fastq,8835694041.0,58517949.0,GSM2776982 r2,0:75.51 1:75.48,A:2524661133;C:1502485662;G:1635422368;T:3172516743;N:608135,75,75,,,2524661133,1502485662,1635422368,3172516743,608135,SRX3171487,SRS2501295,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.37169,0.69933,0.33104,0.59253,0.93659,0.82836,0.49319,0.51176,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43509,SRR6020419,SRX3171487,SRS2501295,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Trans,GSM2776982,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776982,GSM2776982: R4 terv Trans; Danio rerio; RNA Seq,GSM2776982,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Trans_p03_R1.fastq.gz R4_terv_Trans_p03_R2.fastq.gz,fastq fastq,4386400893.0,29067702.0,GSM2776982 r3,0:75.49 1:75.41,A:1326956065;C:724491767;G:749677156;T:1585148439;N:127466,75,75,,,1326956065,724491767,749677156,1585148439,127466,SRX3171487,SRS2501295,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.31136,0.62851,0.26305,0.46553,0.95517,0.87024,0.52178,0.52923,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43510,SRR6020420,SRX3171487,SRS2501295,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Trans,GSM2776982,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776982,GSM2776982: R4 terv Trans; Danio rerio; RNA Seq,GSM2776982,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Trans_p04_R1.fastq.gz R4_terv_Trans_p04_R2.fastq.gz,fastq fastq,9245152121.0,61263899.0,GSM2776982 r4,0:75.46 1:75.45,A:2833957542;C:1482543934;G:1582652549;T:3345945412;N:52684,75,75,,,2833957542,1482543934,1582652549,3345945412,52684,SRX3171487,SRS2501295,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33283,0.69016,0.28123,0.49239,0.95039,0.83437,0.49598,0.54367,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43511,SRR6020413,SRX3171486,SRS2501296,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Scar,GSM2776981,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776981,GSM2776981: R4 terv Scar; Danio rerio; RNA Seq,GSM2776981,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Scar_p01_R1.fastq.gz R4_terv_Scar_p01_R2.fastq.gz,fastq fastq,63013537.0,414730.0,GSM2776981 r1,0:75.98 1:75.96,A:11340679;C:18348371;G:23382873;T:9940711;N:903,75,75,,,11340679,18348371,23382873,9940711,903,SRX3171486,SRS2501296,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0005,0.0001,0.00026,7e-05,0.99993,0.99995,0.05882,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43512,SRR6020414,SRX3171486,SRS2501296,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Scar,GSM2776981,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776981,GSM2776981: R4 terv Scar; Danio rerio; RNA Seq,GSM2776981,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Scar_p02_R1.fastq.gz R4_terv_Scar_p02_R2.fastq.gz,fastq fastq,118778173.0,782191.0,GSM2776981 r2,0:75.93 1:75.92,A:22484503;C:33087570;G:42161784;T:21035442;N:8874,75,75,,,22484503,33087570,42161784,21035442,8874,SRX3171486,SRS2501296,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.02075,0.05067,0.01832,0.04276,0.99279,0.97654,0.44392,0.52218,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43513,SRR6020415,SRX3171486,SRS2501296,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Scar,GSM2776981,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776981,GSM2776981: R4 terv Scar; Danio rerio; RNA Seq,GSM2776981,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Scar_p03_R1.fastq.gz R4_terv_Scar_p03_R2.fastq.gz,fastq fastq,713249164.0,4694227.0,GSM2776981 r3,0:75.98 1:75.96,A:125818684;C:207435216;G:268732472;T:111244414;N:18378,75,75,,,125818684,207435216,268732472,111244414,18378,SRX3171486,SRS2501296,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,1e-05,1e-05,0.0,0.99997,1.0,0.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43514,SRR6020416,SRX3171486,SRS2501296,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terv Scar,GSM2776981,,source name:tertiary ventral fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terv Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary ventral fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776981,GSM2776981: R4 terv Scar; Danio rerio; RNA Seq,GSM2776981,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terv_Scar_p04_R1.fastq.gz R4_terv_Scar_p04_R2.fastq.gz,fastq fastq,483844486.0,3184595.0,GSM2776981 r4,0:75.98 1:75.95,A:85646205;C:140894435;G:180981122;T:76320328;N:2396,75,75,,,85646205,140894435,180981122,76320328,2396,SRX3171486,SRS2501296,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0003,0.00067,0.00018,0.00046,0.99989,0.99935,0.15,0.41176,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43515,SRR6020409,SRX3171485,SRS2501294,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Trans,GSM2776980,,source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776980,GSM2776980: R4 terd Trans; Danio rerio; RNA Seq,GSM2776980,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Trans_p01_R1.fastq.gz R4_terd_Trans_p01_R2.fastq.gz,fastq fastq,9353477829.0,61985103.0,GSM2776980 r1,0:75.45 1:75.45,A:2918476093;C:1414091678;G:1474868294;T:3545988622;N:53142,75,75,,,2918476093,1414091678,1474868294,3545988622,53142,SRX3171485,SRS2501294,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.36441,0.7593,0.31336,0.55295,0.95093,0.82292,0.49914,0.53019,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43516,SRR6020410,SRX3171485,SRS2501294,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Trans,GSM2776980,,source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776980,GSM2776980: R4 terd Trans; Danio rerio; RNA Seq,GSM2776980,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Trans_p02_R1.fastq.gz R4_terd_Trans_p02_R2.fastq.gz,fastq fastq,6626365664.0,43908545.0,GSM2776980 r2,0:75.44 1:75.47,A:1980665411;C:1019945066;G:1082628078;T:2543089101;N:38008,75,75,,,1980665411,1019945066,1082628078,2543089101,38008,SRX3171485,SRS2501294,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.32749,0.78639,0.25705,0.43545,0.95745,0.82,0.5,0.52298,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43517,SRR6020411,SRX3171485,SRS2501294,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Trans,GSM2776980,,source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776980,GSM2776980: R4 terd Trans; Danio rerio; RNA Seq,GSM2776980,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Trans_p03_R1.fastq.gz R4_terd_Trans_p03_R2.fastq.gz,fastq fastq,250213383.0,1657189.0,GSM2776980 r3,0:75.51 1:75.48,A:70872645;C:40721033;G:44641734;T:93961355;N:16616,75,75,,,70872645,40721033,44641734,93961355,16616,SRX3171485,SRS2501294,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.39985,0.75081,0.34725,0.58284,0.93975,0.82116,0.49709,0.51312,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43518,SRR6020412,SRX3171485,SRS2501294,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Trans,GSM2776980,,source name:tertiary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,tertiary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776980,GSM2776980: R4 terd Trans; Danio rerio; RNA Seq,GSM2776980,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Trans_p04_R1.fastq.gz R4_terd_Trans_p04_R2.fastq.gz,fastq fastq,2439737928.0,16175327.0,GSM2776980 r4,0:75.43 1:75.40,A:791363066;C:393366804;G:387269134;T:867699009;N:39915,75,75,,,791363066,393366804,387269134,867699009,39915,SRX3171485,SRS2501294,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.41064,0.68389,0.36279,0.60184,0.94801,0.91321,0.50483,0.5018,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43519,SRR6020405,SRX3171484,SRS2501293,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Scar,GSM2776979,,source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,teritary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776979,GSM2776979: R4 terd Scar; Danio rerio; RNA Seq,GSM2776979,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Scar_p01_R1.fastq.gz R4_terd_Scar_p01_R2.fastq.gz,fastq fastq,472339159.0,3108723.0,GSM2776979 r1,0:75.98 1:75.96,A:83061434;C:137317024;G:178719638;T:73238676;N:2387,75,75,,,83061434,137317024,178719638,73238676,2387,SRX3171484,SRS2501293,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00033,0.00025,0.0002,0.00013,0.99993,0.99963,0.0,0.61111,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43520,SRR6020406,SRX3171484,SRS2501293,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Scar,GSM2776979,,source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,teritary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776979,GSM2776979: R4 terd Scar; Danio rerio; RNA Seq,GSM2776979,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Scar_p02_R1.fastq.gz R4_terd_Scar_p02_R2.fastq.gz,fastq fastq,405913408.0,2671239.0,GSM2776979 r2,0:75.99 1:75.97,A:71703296;C:117980100;G:153764667;T:62463222;N:2123,75,75,,,71703296,117980100,153764667,62463222,2123,SRX3171484,SRS2501293,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,0.00011,1e-05,4e-05,0.99993,0.99981,0.66666,0.7,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43521,SRR6020407,SRX3171484,SRS2501293,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Scar,GSM2776979,,source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,teritary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776979,GSM2776979: R4 terd Scar; Danio rerio; RNA Seq,GSM2776979,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Scar_p03_R1.fastq.gz R4_terd_Scar_p03_R2.fastq.gz,fastq fastq,35300008.0,232328.0,GSM2776979 r3,0:75.97 1:75.97,A:6443488;C:10004950;G:13144621;T:5704811;N:2138,75,75,,,6443488,10004950,13144621,5704811,2138,SRX3171484,SRS2501293,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00275,0.00097,0.00214,0.00083,0.99943,0.99955,0.15454,0.52173,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43522,SRR6020408,SRX3171484,SRS2501293,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 terd Scar,GSM2776979,,source name:teritary dorsal fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,R4 terd Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,teritary dorsal fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:tertiary fin|sorted plates:4,GSM2776979,GSM2776979: R4 terd Scar; Danio rerio; RNA Seq,GSM2776979,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_terd_Scar_p04_R1.fastq.gz R4_terd_Scar_p04_R2.fastq.gz,fastq fastq,35300008.0,232328.0,GSM2776979 r4,0:75.97 1:75.97,A:6443488;C:10004950;G:13144621;T:5704811;N:2138,75,75,,,6443488,10004950,13144621,5704811,2138,SRX3171484,SRS2501293,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00276,0.00097,0.00213,0.00082,0.99945,0.99949,0.14035,0.53846,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43523,SRR6020399,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p01_R1.fastq.gz R4_sec_Trans_p01_R2.fastq.gz,fastq fastq,7943223694.0,52632584.0,GSM2776978 r1,0:75.50 1:75.42,A:2426047253;C:1345760701;G:1411992441;T:2757726644;N:1696655,75,75,,,2426047253,1345760701,1411992441,2757726644,1696655,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.39936,0.64405,0.35361,0.55608,0.91311,0.84431,0.5165,0.52376,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43524,SRR6020400,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p02_R1.fastq.gz R4_sec_Trans_p02_R2.fastq.gz,fastq fastq,8875571511.0,58802279.0,GSM2776978 r2,0:75.52 1:75.42,A:2702312372;C:1527849144;G:1608513066;T:3034988415;N:1908514,75,75,,,2702312372,1527849144,1608513066,3034988415,1908514,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.38955,0.61673,0.34428,0.5327,0.91774,0.85094,0.50279,0.51953,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43525,SRR6020401,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p03_R1.fastq.gz R4_sec_Trans_p03_R2.fastq.gz,fastq fastq,10196306186.0,67549716.0,GSM2776978 r3,0:75.48 1:75.47,A:3021055822;C:1591602601;G:1717130650;T:3866184067;N:333046,75,75,,,3021055822,1591602601,1717130650,3866184067,333046,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.42177,0.73274,0.37881,0.60342,0.93845,0.83104,0.49961,0.48288,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43526,SRR6020402,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p04_R1.fastq.gz R4_sec_Trans_p04_R2.fastq.gz,fastq fastq,16321632703.0,108129317.0,GSM2776978 r4,0:75.48 1:75.47,A:4839288181;C:2524952022;G:2722722795;T:6234157991;N:511714,75,75,,,4839288181,2524952022,2722722795,6234157991,511714,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.43062,0.74617,0.38255,0.59574,0.93693,0.8256,0.50653,0.53888,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43527,SRR6020403,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p05_R1.fastq.gz R4_sec_Trans_p05_R2.fastq.gz,fastq fastq,8368447970.0,55444521.0,GSM2776978 r5,0:75.47 1:75.46,A:2470524458;C:1322545235;G:1459320910;T:3115796506;N:260861,75,75,,,2470524458,1322545235,1459320910,3115796506,260861,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.38066,0.70664,0.33844,0.56193,0.94134,0.82846,0.48774,0.47937,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43528,SRR6020404,SRX3171483,SRS2501292,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Trans,GSM2776978,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776978,GSM2776978: R4 sec Trans; Danio rerio; RNA Seq,GSM2776978,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Trans_p06_R1.fastq.gz R4_sec_Trans_p06_R2.fastq.gz,fastq fastq,9774461624.0,64760766.0,GSM2776978 r6,0:75.47 1:75.46,A:2902527714;C:1488941576;G:1661506049;T:3721177113;N:309172,75,75,,,2902527714,1488941576,1661506049,3721177113,309172,SRX3171483,SRS2501292,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.39334,0.71354,0.35122,0.56253,0.94513,0.84628,0.47779,0.55996,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43529,SRR6020393,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p01_R1.fastq.gz R4_sec_Scar_p01_R2.fastq.gz,fastq fastq,443752860.0,2921141.0,GSM2776977 r1,0:75.98 1:75.93,A:78584919;C:129545943;G:166851959;T:68680115;N:89924,75,75,,,78584919,129545943,166851959,68680115,89924,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00014,0.00018,9e-05,0.00013,0.99991,0.99985,0.4,0.57142,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43530,SRR6020394,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p02_R1.fastq.gz R4_sec_Scar_p02_R2.fastq.gz,fastq fastq,609377510.0,4011701.0,GSM2776977 r2,0:75.99 1:75.91,A:108185883;C:176784326;G:229824363;T:94453370;N:129568,75,75,,,108185883,176784326,229824363,94453370,129568,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,6e-05,0.0001,5e-05,7e-05,1.0,0.99991,,0.25,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43531,SRR6020395,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p03_R1.fastq.gz R4_sec_Scar_p03_R2.fastq.gz,fastq fastq,695786067.0,4580703.0,GSM2776977 r3,0:75.98 1:75.91,A:122056429;C:202686271;G:262426973;T:108597814;N:18580,75,75,,,122056429,202686271,262426973,108597814,18580,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00035,0.00084,0.00028,0.00068,0.99981,0.99955,0.18181,0.45454,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43532,SRR6020396,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p04_R1.fastq.gz R4_sec_Scar_p04_R2.fastq.gz,fastq fastq,468236053.0,3082347.0,GSM2776977 r4,0:75.98 1:75.92,A:82822403;C:136423938;G:175959465;T:73018299;N:11948,75,75,,,82822403,136423938,175959465,73018299,11948,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,7e-05,1e-05,3e-05,0.99997,0.99991,0.0,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43533,SRR6020397,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p05_R1.fastq.gz R4_sec_Scar_p05_R2.fastq.gz,fastq fastq,494012269.0,3251619.0,GSM2776977 r5,0:75.98 1:75.94,A:87398485;C:143668568;G:186485697;T:76445953;N:13566,75,75,,,87398485,143668568,186485697,76445953,13566,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,8e-05,7e-05,4e-05,1e-05,0.99991,0.99985,0.2,0.71428,76,75,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43534,SRR6020398,SRX3171482,SRS2501291,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 sec Scar,GSM2776977,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,R4 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:secondary fin|sorted plates:6,GSM2776977,GSM2776977: R4 sec Scar; Danio rerio; RNA Seq,GSM2776977,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_sec_Scar_p06_R1.fastq.gz R4_sec_Scar_p06_R2.fastq.gz,fastq fastq,488664520.0,3216541.0,GSM2776977 r6,0:75.98 1:75.94,A:86623588;C:141946345;G:183757005;T:76325350;N:12232,75,75,,,86623588,141946345,183757005,76325350,12232,SRX3171482,SRS2501291,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0001,0.00015,5e-05,8e-05,0.99991,0.99983,0.16666,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43535,SRR6020387,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p01_R1.fastq.gz R4_prim_Trans_p01_R2.fastq.gz,fastq fastq,4156649914.0,27498834.0,GSM2776976 r1,0:75.66 1:75.50,A:1184667722;C:812111779;G:946047137;T:1213491214;N:332062,75,75,,,1184667722,812111779,946047137,1213491214,332062,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.13191,0.27606,0.11079,0.21313,0.97981,0.95864,0.48952,0.51323,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43536,SRR6020388,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p02_R1.fastq.gz R4_prim_Trans_p02_R2.fastq.gz,fastq fastq,5961095878.0,39431358.0,GSM2776976 r2,0:75.66 1:75.51,A:1678045732;C:1185915367;G:1391829821;T:1704836561;N:468397,75,75,,,1678045732,1185915367,1391829821,1704836561,468397,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.13017,0.27029,0.11004,0.21778,0.9795,0.95978,0.54044,0.51146,76,76,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43537,SRR6020389,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p03_R1.fastq.gz R4_prim_Trans_p03_R2.fastq.gz,fastq fastq,6170232577.0,40846092.0,GSM2776976 r3,0:75.56 1:75.50,A:1866777846;C:1148020988;G:1151073641;T:2003993265;N:366837,75,75,,,1866777846,1148020988,1151073641,2003993265,366837,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.21204,0.40881,0.18286,0.33189,0.95931,0.9108,0.49141,0.53253,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43538,SRR6020390,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p04_R1.fastq.gz R4_prim_Trans_p04_R2.fastq.gz,fastq fastq,11725606474.0,77611342.0,GSM2776976 r4,0:75.62 1:75.46,A:3255674293;C:2567072026;G:2847190480;T:3054954945;N:714730,75,75,,,3255674293,2567072026,2847190480,3054954945,714730,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.06986,0.13983,0.05982,0.11888,0.98516,0.97161,0.49686,0.4638,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43539,SRR6020391,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p05_R1.fastq.gz R4_prim_Trans_p05_R2.fastq.gz,fastq fastq,10721896827.0,71080622.0,GSM2776976 r5,0:75.44 1:75.41,A:3568478635;C:1747554798;G:1675757438;T:3729472140;N:633816,75,75,,,3568478635,1747554798,1675757438,3729472140,633816,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.32298,0.52706,0.28009,0.43701,0.94349,0.90078,0.51345,0.52304,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43540,SRR6020392,SRX3171481,SRS2501290,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Trans,GSM2776976,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776976,GSM2776976: R4 prim Trans; Danio rerio; RNA Seq,GSM2776976,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Trans_p06_R1.fastq.gz R4_prim_Trans_p06_R2.fastq.gz,fastq fastq,4861560177.0,32218130.0,GSM2776976 r6,0:75.46 1:75.44,A:1606516776;C:766379277;G:687731226;T:1800636189;N:296709,75,75,,,1606516776,766379277,687731226,1800636189,296709,SRX3171481,SRS2501290,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.40198,0.66219,0.35056,0.55779,0.94671,0.8913,0.48395,0.50179,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43541,SRR6020381,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p01_R1.fastq.gz R4_prim_Scar_p01_R2.fastq.gz,fastq fastq,2115181733.0,13930610.0,GSM2776975 r1,0:75.96 1:75.88,A:379992687;C:608145647;G:806462037;T:320430832;N:150530,75,75,,,379992687,608145647,806462037,320430832,150530,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,4e-05,2e-05,2e-05,1.0,0.99997,,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43542,SRR6020382,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p02_R1.fastq.gz R4_prim_Scar_p02_R2.fastq.gz,fastq fastq,1500850853.0,9884525.0,GSM2776975 r2,0:75.96 1:75.88,A:272764495;C:429257065;G:572879423;T:225831427;N:118443,75,75,,,272764495,429257065,572879423,225831427,118443,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0,3e-05,0.0,1e-05,1.0,0.99997,,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43543,SRR6020383,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p03_R1.fastq.gz R4_prim_Scar_p03_R2.fastq.gz,fastq fastq,1802726164.0,11867972.0,GSM2776975 r3,0:75.98 1:75.91,A:320691778;C:528568175;G:676214104;T:277152518;N:99589,75,75,,,320691778,528568175,676214104,277152518,99589,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,1e-05,0.0,0.0,0.0,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43544,SRR6020384,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p04_R1.fastq.gz R4_prim_Scar_p04_R2.fastq.gz,fastq fastq,1589218979.0,10459351.0,GSM2776975 r4,0:75.98 1:75.96,A:284759473;C:465370937;G:594649808;T:244354408;N:84353,75,75,,,284759473,465370937,594649808,244354408,84353,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,8e-05,2e-05,6e-05,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43545,SRR6020385,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p05_R1.fastq.gz R4_prim_Scar_p05_R2.fastq.gz,fastq fastq,1044289567.0,6872484.0,GSM2776975 r5,0:75.99 1:75.97,A:180521535;C:302898685;G:398946567;T:161866241;N:56539,75,75,,,180521535,302898685,398946567,161866241,56539,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0,2e-05,0.0,1e-05,1.0,1.0,,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43546,SRR6020386,SRX3171480,SRS2501289,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R4 prim Scar,GSM2776975,,source name:primary fin single cells|cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,R4 prim Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R4|tissue:primary fin|sorted plates:6,GSM2776975,GSM2776975: R4 prim Scar; Danio rerio; RNA Seq,GSM2776975,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R4_prim_Scar_p06_R1.fastq.gz R4_prim_Scar_p06_R2.fastq.gz,fastq fastq,1191573683.0,7850142.0,GSM2776975 r6,0:75.98 1:75.81,A:222979447;C:342633187;G:444672356;T:181222920;N:65773,75,75,,,222979447,342633187,444672356,181222920,65773,SRX3171480,SRS2501289,SRA602108,GEO,"AVO, Hubrecht Institue",2,3e-05,0.0,1e-05,0.0,0.99997,1.0,1.0,,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43623,SRR5961766,SRX3119877,SRS2454736,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 primary fin Scars,GSM2752200,,source name:primary fin single cells|cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2,P1 primary fin Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing 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:primary fin|sorted plates:2,GSM2752200,GSM2752200: P1 primary fin Scars; Danio rerio; RNA Seq,GSM2752200,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752200,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_fin_Scar_p01_R1.fastq.gz P1_fin_Scar_p01_R2.fastq.gz,fastq fastq,295970986.0,1947440.0,GSM2752200 r1,0:75.99 1:75.99,A:52888700;C:85164846;G:110699732;T:47204092;N:13616,75,75,,,52888700,85164846,110699732,47204092,13616,SRX3119877,SRS2454736,SRA602108,GEO,"AVO, Hubrecht Institue",2,4e-05,3e-05,2e-05,0.0,0.99995,0.99991,0.5,0.25,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Fin,Surface Structure
43624,SRR5961767,SRX3119877,SRS2454736,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 primary fin Scars,GSM2752200,,source name:primary fin single cells|cas9 injection:protein|FISH id:P1|tissue:primary fin|sorted plates:2,P1 primary fin Scars,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to  1; and extending gap penalty to  0.1. Subsequently  we pool scars per cell and by cigar. For each scar library  a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next  scars were filtered according to their frequency of detection in the full library. For each cell  reads are normalized to 100 and scars representing less than 3.5% are removed.                                        Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing 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:primary fin|sorted plates:2,GSM2752200,GSM2752200: P1 primary fin Scars; Danio rerio; RNA Seq,GSM2752200,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2752200,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P1_fin_Scar_p02_R1.fastq.gz P1_fin_Scar_p02_R2.fastq.gz,fastq fastq,663461589.0,4365910.0,GSM2752200 r2,0:75.98 1:75.99,A:121052549;C:188284261;G:244595786;T:109498791;N:30202,75,75,,,121052549,188284261,244595786,109498791,30202,SRX3119877,SRS2454736,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00271,0.00078,0.00264,0.00075,0.99997,0.99997,0.0,0.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-08-23,Undetermined,Multi-stage,Fin,Surface Structure
52177,SRR10902870,SRX7571040,SRS6006641,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin 6,GSM4274616,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 6,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274616,GSM4274616: CaudalFin 6; Danio rerio; RNA Seq,GSM4274616,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274616,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin6.bam,bam,15182183400.0,50607278.0,GSM4274616 r1,0:150 1:150,A:3885671292;C:2808118660;G:2749433455;T:5736812768;N:2147225,150,150,,,3885671292,2808118660,2749433455,5736812768,2147225,SRX7571040,SRS6006641,SRA880843,GEO,Zhejiang University,2,0.0,0.75585,0.0,0.03963,1.0,0.85683,,0.66839,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure
52178,SRR10902869,SRX7571039,SRS6006640,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin 5,GSM4274615,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 5,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274615,GSM4274615: CaudalFin 5; Danio rerio; RNA Seq,GSM4274615,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274615,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin5.bam,bam,12714687300.0,42382291.0,GSM4274615 r1,0:150 1:150,A:3251897336;C:2310288259;G:2258210415;T:4892500201;N:1791089,150,150,,,3251897336,2310288259,2258210415,4892500201,1791089,SRX7571039,SRS6006640,SRA880843,GEO,Zhejiang University,2,0.0,0.72038,0.0,0.03882,1.0,0.86032,,0.62044,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure
52179,SRR10902868,SRX7571038,SRS6006639,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin 4,GSM4274614,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 4,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274614,GSM4274614: CaudalFin 4; Danio rerio; RNA Seq,GSM4274614,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274614,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin4.bam,bam,11693371200.0,38977904.0,GSM4274614 r1,0:150 1:150,A:3057191149;C:2115231923;G:2060789562;T:4458505458;N:1653108,150,150,,,3057191149,2115231923,2060789562,4458505458,1653108,SRX7571038,SRS6006639,SRA880843,GEO,Zhejiang University,2,0.0,0.69243,0.0,0.02868,1.0,0.86801,,0.58425,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure
52180,SRR10902867,SRX7571037,SRS6006638,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin 3,GSM4274613,,source name:caudal fin|strain:Tubingen|tissue:caudal fin|genotype:wild type,CaudalFin 3,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:caudal fin|genotype:wild type,GSM4274613,GSM4274613: CaudalFin 3; Danio rerio; RNA Seq,GSM4274613,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM4274613,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:GRCz10|intentional duplicate,CaudalFin3.bam,bam,15450513000.0,51501710.0,GSM4274613 r1,0:150 1:150,A:4147311733;C:2703423917;G:2642017355;T:5955551498;N:2208497,150,150,,,4147311733,2703423917,2642017355,5955551498,2208497,SRX7571037,SRS6006638,SRA880843,GEO,Zhejiang University,2,3e-05,0.65311,0.0,0.03421,0.99997,0.8774,0.0,0.57684,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2020-01-16,Undetermined,Multi-stage,Fin,Surface Structure
52191,SRR9058956,SRX5835156,SRS4761452,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin1,GSM3768153,,source name:caudal fin|strain:Tubingen|genotype/variation:wild type|tissue:caudal fin,CaudalFin1,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:caudal fin,GSM3768153,GSM3768153: CaudalFin1; Danio rerio; RNA Seq,GSM3768153,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768153,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,CaudalFin1.bam,bam,14329147114.0,47447507.0,GSM3768153 r1,0:151 1:151,A:3440675044;C:2610927283;G:2684180140;T:5590878261;N:2486386,151,151,,,3440675044,2610927283,2684180140,5590878261,2486386,SRX5835156,SRS4761452,SRA880843,GEO,Zhejiang University,2,0.0,0.89661,0.0,0.03373,1.0,0.85821,,0.55774,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Fin,Surface Structure
52208,SRR8991396,SRX5770464,SRS4704573,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,CaudalFin2,GSM3740949,,source name:caudal fin|strain:Tubingen|genotype:wild type|tissue:caudal fin,CaudalFin2,The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,caudal fin,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:caudal fin,GSM3740949,GSM3740949: CaudalFin2; Danio rerio; RNA Seq,GSM3740949,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,CaudalFin2.bam,bam,34657911996.0,114761298.0,GSM3740949 r1,0:151 1:151,A:8439354130;C:5842860159;G:6009391550;T:14359478869;N:6827288,151,151,,,8439354130,5842860159,6009391550,14359478869,6827288,SRX5770464,SRS4704573,SRA880843,GEO,Zhejiang University,2,2e-05,0.79468,0.0,0.03917,0.99997,0.86393,0.0,0.58978,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Fin,Surface Structure
52209,SRR8992787,SRX5771765,SRS4705624,SRP194294,PRJNA540521,Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores,GSE130526,Other,Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates  derived from embryonic neural crest  are a useful system for elucidating mechanisms of fate specification  pattern formation  and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes  including zebrafish Danio rerio  we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic  mutational  chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions  organelle configurations and genetic requirements. At the organismal level  we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together  our studies revealed new  independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish  and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication,,pubmed:31138706,,Zebrafish fin pigment cells,GSM3741778,,tissue:Dorsal and anal fins|cell type:pigment cells|treatment:Untreated,Zebrafish fin pigment cells,Expression matrix files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.,Dorsal and anal fins,Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation  we extracted distal dorsal fin regions 10 mm standard length  SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL  15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels  single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A  FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence  and then cells from transgenic fish were purified according to these gates. All samples were kept on ice  except during Liberase incubation  and then sorted chilled.,10X genomics V1 protocol following manufacturer recommendations.,Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb  a derivative of inbred ABwp  Tgtyrp1b:palm mCherrywp.rt11  Tgpnp4a:palmmCherrywp.rt10,cell type:pigment cells|treatment:Untreated,GSM3741778,GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq,GSM3741778,,1,10X genomics V1 protocol following manufacturer recommendations.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP194294,,,leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz,fastq fastq,424061944.0,10241510.0,GSM3741778 r1,0:26 1:57,A:119042142;C:89897538;G:98172861;T:116716009;N:233394,26,57,,,119042142,89897538,98172861,116716009,233394,SRX5771765,SRS4705624,SRA881136,GEO,"Parichy Lab, Biology, University of Washington",1,0.33934,,0.07693,,0.8742,,0.51425,,57,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2019-04-30,Multi-stage,Multi-stage,Fin,Surface Structure
58389,SRR11486781,SRX8062812,SRS6431234,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1,GSM4455083,,source name:whole fin|date:2 dpa|tissue:whole fin,RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:2 dpa|tissue:whole fin,GSM4455083,GSM4455083: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455083,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455083,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S8_S75_L008_R1_001.fastq.gz,fastq,2464411341.0,48321791.0,GSM4455083 r1,0:51 1:0,A:620643336;C:590840801;G:549905028;T:702758180;N:263996,51,0,,,620643336,590840801,549905028,702758180,263996,SRX8062812,SRS6431234,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91677,,0.09917,,0.71981,,0.46761,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58390,SRR11486780,SRX8062811,SRS6431233,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 2dpa; injured; batch 3; rep1,GSM4455082,,source name:whole fin|date:2 dpa|tissue:whole fin,RNAseq; whole fin; 2dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:2 dpa|tissue:whole fin,GSM4455082,GSM4455082: RNAseq; whole fin; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455082,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455082,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S6_S73_L008_R1_001.fastq.gz,fastq,2567417214.0,50341514.0,GSM4455082 r1,0:51 1:0,A:648888081;C:617286062;G:571907197;T:729086777;N:249097,51,0,,,648888081,617286062,571907197,729086777,249097,SRX8062811,SRS6431233,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91819,,0.10483,,0.72062,,0.45077,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58391,SRR11486779,SRX8062810,SRS6431232,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1,GSM4455081,,source name:whole fin|date:0 dpa|tissue:whole fin,RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:0 dpa|tissue:whole fin,GSM4455081,GSM4455081: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455081,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455081,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S7_S74_L008_R1_001.fastq.gz,fastq,2644840467.0,51859617.0,GSM4455081 r1,0:51 1:0,A:676588053;C:621109147;G:581574642;T:765307978;N:260647,51,0,,,676588053,621109147,581574642,765307978,260647,SRX8062810,SRS6431232,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.89598,,0.1281,,0.71417,,0.47147,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58392,SRR11486778,SRX8062809,SRS6431231,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1,GSM4455080,,source name:whole fin|date:0 dpa|tissue:whole fin,RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,whole fin,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,date:0 dpa|tissue:whole fin,GSM4455080,GSM4455080: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4455080,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.,GEO Accession:GSM4455080,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,JK-S5_S72_L008_R1_001.fastq.gz,fastq,2412481254.0,47303554.0,GSM4455080 r1,0:51 1:0,A:616219239;C:570826024;G:531833820;T:693353914;N:248257,51,0,,,616219239,570826024,531833820,693353914,248257,SRX8062809,SRS6431231,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.90059,,0.11572,,0.72013,,0.46152,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-04-06,Multi-stage,Multi-stage,Fin,Surface Structure
58393,SRR11305419,SRX7910559,SRS6318068,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2,GSM4411419,,source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:fibroblast|genotype:wild type,GSM4411419,GSM4411419: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2; Danio rerio; RNA Seq,GSM4411419,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411419,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_injured_Regen_B2_S60_L008_R1_001.fastq.gz,fastq,3284939427.0,64410577.0,GSM4411419 r1,0:51 1:0,A:903305689;C:745606629;G:745227959;T:890156683;N:642467,51,0,,,903305689,745606629,745227959,890156683,642467,SRX7910559,SRS6318068,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92145,,0.11147,,0.75091,,0.47874,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58394,SRR11305418,SRX7910558,SRS6318067,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1,GSM4411418,,source name:RNAseq; Fibroblast; 4dpi; injured|time:4 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:fibroblast|genotype:wild type,GSM4411418,GSM4411418: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1; Danio rerio; RNA Seq,GSM4411418,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411418,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_injured_Regen_A2_S59_L008_R1_001.fastq.gz,fastq,3208227063.0,62906413.0,GSM4411418 r1,0:51 1:0,A:889970085;C:720088600;G:719685444;T:877865381;N:617553,51,0,,,889970085,720088600,719685444,877865381,617553,SRX7910558,SRS6318067,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91814,,0.12108,,0.74704,,0.51875,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58395,SRR11305417,SRX7910557,SRS6318066,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2,GSM4411417,,source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:fibroblast|genotype:wild type,GSM4411417,GSM4411417: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2; Danio rerio; RNA Seq,GSM4411417,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411417,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_uninjured_Uninj_B2_S58_L008_R1_001.fastq.gz,fastq,3779977251.0,74117201.0,GSM4411417 r1,0:51 1:0,A:1036587583;C:863955138;G:859693317;T:1019029136;N:712077,51,0,,,1036587583,863955138,859693317,1019029136,712077,SRX7910557,SRS6318066,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91762,,0.12285,,0.7683,,0.47877,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58396,SRR11305416,SRX7910556,SRS6318065,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1,GSM4411416,,source name:RNAseq; Fibroblast; 0dpi; uninjured|time:0 dpa|tissue:fibroblast|genotype:wild type,RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; Fibroblast; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:fibroblast|genotype:wild type,GSM4411416,GSM4411416: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq,GSM4411416,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411416,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,Fibro.RNAseq_uninjured_Uninj_A2_S57_L008_R1_001.fastq.gz,fastq,3830264271.0,75103221.0,GSM4411416 r1,0:51 1:0,A:1040171853;C:881400891;G:878214685;T:1029746894;N:729948,51,0,,,1040171853,881400891,878214685,1029746894,729948,SRX7910556,SRS6318065,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92032,,0.09358,,0.75771,,0.4712,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58397,SRR11305415,SRX7910555,SRS6318064,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep3,GSM4411415,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411415,GSM4411415: RNAseq; whole fin; 1dpa; injured; batch 2; rep3; Danio rerio; RNA Seq,GSM4411415,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411415,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_A_S37_L004_R1_001.fastq.gz,fastq,2924051085.0,57334335.0,GSM4411415 r1,0:51 1:0,A:678403251;C:734140605;G:692166374;T:819274692;N:66163,51,0,,,678403251,734140605,692166374,819274692,66163,SRX7910555,SRS6318064,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.93427,,0.06589,,0.73866,,0.45737,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58398,SRR11305414,SRX7910554,SRS6318063,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep2,GSM4411414,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411414,GSM4411414: RNAseq; whole fin; 1dpa; injured; batch 2; rep2; Danio rerio; RNA Seq,GSM4411414,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411414,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_B_S38_L004_R1_001.fastq.gz,fastq,3159176895.0,61944645.0,GSM4411414 r1,0:51 1:0,A:730026525;C:803379127;G:747179794;T:878521357;N:70092,51,0,,,730026525,803379127,747179794,878521357,70092,SRX7910554,SRS6318063,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.93516,,0.07492,,0.74602,,0.46646,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58399,SRR11305413,SRX7910553,SRS6318062,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 1dpa; injured; batch 2; rep1,GSM4411413,,source name:RNAseq; whole fin; 1dpi; injured|time:1 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 1dpa; injured; batch 2; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 1dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:1 dpa|tissue:whole fin|genotype:wild type,GSM4411413,GSM4411413: RNAseq; whole fin; 1dpa; injured; batch 2; rep1; Danio rerio; RNA Seq,GSM4411413,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411413,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_injured_RNA_1dpa_C_S39_L004_R1_001.fastq.gz,fastq,3053752296.0,59877496.0,GSM4411413 r1,0:51 1:0,A:705251373;C:775521263;G:724421121;T:848486693;N:71846,51,0,,,705251373,775521263,724421121,848486693,71846,SRX7910553,SRS6318062,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.9345,,0.08171,,0.74326,,0.47043,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58400,SRR11305412,SRX7910552,SRS6318061,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3,GSM4411412,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411412,GSM4411412: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3; Danio rerio; RNA Seq,GSM4411412,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411412,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_B_S35_L004_R1_001.fastq.gz,fastq,3095170620.0,60689620.0,GSM4411412 r1,0:51 1:0,A:728515579;C:769711604;G:717419279;T:879450837;N:73321,51,0,,,728515579,769711604,717419279,879450837,73321,SRX7910552,SRS6318061,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91314,,0.09911,,0.72498,,0.46006,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58401,SRR11305411,SRX7910551,SRS6318060,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2,GSM4411411,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411411,GSM4411411: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2; Danio rerio; RNA Seq,GSM4411411,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411411,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_C_S36_L004_R1_001.fastq.gz,fastq,2959811163.0,58035513.0,GSM4411411 r1,0:51 1:0,A:702000960;C:731163416;G:687625038;T:838953116;N:68633,51,0,,,702000960,731163416,687625038,838953116,68633,SRX7910551,SRS6318060,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91317,,0.09909,,0.7237,,0.45771,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58402,SRR11305410,SRX7910550,SRS6318059,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1,GSM4411410,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411410,GSM4411410: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1; Danio rerio; RNA Seq,GSM4411410,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411410,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin1dpi.RNAseq_uninjured_RNA_0dpa_A_S34_L004_R1_001.fastq.gz,fastq,2850762963.0,55897313.0,GSM4411410 r1,0:51 1:0,A:675289993;C:707558547;G:662291002;T:805558844;N:64577,51,0,,,675289993,707558547,662291002,805558844,64577,SRX7910550,SRS6318059,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91288,,0.10801,,0.72165,,0.46866,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58403,SRR11305409,SRX7910549,SRS6318058,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 4dpa; injured; batch 1; rep2,GSM4411409,,source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 4dpa; injured; batch 1; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:whole fin|genotype:wild type,GSM4411409,GSM4411409: RNAseq; whole fin; 4dpa; injured; batch 1; rep2; Danio rerio; RNA Seq,GSM4411409,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411409,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_injured_reg2.fastq.gz,fastq,2523651950.0,50473039.0,GSM4411409 r1,0:50,A:658848054;C:605884052;G:596099791;T:662690555;N:129498,50,,,,658848054,605884052,596099791,662690555,129498,SRX7910549,SRS6318058,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.91959,,0.07092,,0.70717,,0.45829,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58404,SRR11305408,SRX7910548,SRS6318057,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 4dpa; injured; batch 1; rep1,GSM4411408,,source name:RNAseq; whole fin; 4dpi; injured|time:4 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 4dpa; injured; batch 1; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 4dpi; injured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:4 dpa|tissue:whole fin|genotype:wild type,GSM4411408,GSM4411408: RNAseq; whole fin; 4dpa; injured; batch 1; rep1; Danio rerio; RNA Seq,GSM4411408,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411408,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_injured_reg1.fastq.gz,fastq,2490897750.0,49817955.0,GSM4411408 r1,0:50,A:644634582;C:602186818;G:591877446;T:652072339;N:126565,50,,,,644634582,602186818,591877446,652072339,126565,SRX7910548,SRS6318057,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.92355,,0.06175,,0.71342,,0.46396,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58405,SRR11305407,SRX7910547,SRS6318056,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2,GSM4411407,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411407,GSM4411407: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2; Danio rerio; RNA Seq,GSM4411407,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411407,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_uninjured_Uni2.fastq.gz,fastq,1646067800.0,32921356.0,GSM4411407 r1,0:50,A:433931789;C:391550599;G:380315477;T:440186224;N:83711,50,,,,433931789,391550599,380315477,440186224,83711,SRX7910547,SRS6318056,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.90771,,0.08897,,0.71985,,0.44509,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure
58406,SRR11305406,SRX7910546,SRS6318055,SRP252754,PRJNA612515,Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins,GSE146960,Other,Mammalian genomes likely encode all gene products required to regenerate an amputated limb  yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions  which exist as gene cis regulatory elements. Here  to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration  we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration  and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs  we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes  including fgf20a  cx43  and mdka  with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa  and fibroblast 0 dpa and fibroblast 4 dpa.,,pubmed:32665240,,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1,GSM4411406,,source name:RNAseq; whole fin; 0dpi; uninjured|time:0 dpa|tissue:whole fin|genotype:wild type,RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1,RNA Seq reads were trimmed by Trim Galore 0.6.4  with  q 15 and then mapped with TopHat v 2.1.1  with parameters   b2 very sensitive   no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1  with  q 15 and then mapped with bowtie22.2.5  with parameters   very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph,RNAseq; whole fin; 0dpi; uninjured,For fibroblast libraries  triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al.  2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations  Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016  and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C  and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.,time:0 dpa|tissue:whole fin|genotype:wild type,GSM4411406,GSM4411406: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1; Danio rerio; RNA Seq,GSM4411406,,1,For RNA seq  biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries  biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa  1 dpa  or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al.  2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours  collected in 15 minute increments  then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al.  2013.,GEO Accession:GSM4411406,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP252754,,,WFin.RNAseq_uninjured_Uni1.fastq.gz,fastq,2093137350.0,41862747.0,GSM4411406 r1,0:50,A:539953107;C:505949113;G:500993563;T:546137713;N:103854,50,,,,539953107,505949113,500993563,546137713,103854,SRX7910546,SRS6318055,SRA1054723,GEO,"Poss, Cell Biology, Duke University",1,0.9119,,0.07318,,0.72969,,0.43282,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-13,Multi-stage,Multi-stage,Fin,Surface Structure