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
4359,ERR1427424,ERX1497956,ERS1183258,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#91,SAMEA4012148,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012148|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#91|broker name:ArrayExpress|common name:zebrafish|fsc:25859|gfp:119|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#91|ssc:10090|tissue:Heart|well:C12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#91,LCK 7#91,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25859:fsc|Experimental Factor: 10090:ssc|Experimental Factor: 119:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_91_mod.bam LCK_7_91.cram,bam cram,,,E MTAB 4617:LCK 7#91,0:125 1:125,A:115117295;C:110480558;G:102056870;T:121829131;N:52646,125,125,,,115117295,110480558,102056870,121829131,52646,ERX1497956,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.2053,0.20024,0.06111,0.05989,0.98019,0.98058,0.56103,0.56868,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4360,ERR1427423,ERX1497955,ERS1183257,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#90,SAMEA4012147,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012147|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#90|broker name:ArrayExpress|common name:zebrafish|fsc:22987|gfp:178|individual:2|pi:6|plate:7|sample name:E MTAB 4617:LCK 7#90|ssc:6327|tissue:Heart|well:B12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#90,LCK 7#90,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 22987:fsc|Experimental Factor: 6327:ssc|Experimental Factor: 178:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_90_mod.bam LCK_7_90.cram,bam cram,,,E MTAB 4617:LCK 7#90,0:125 1:125,A:106342222;C:98049090;G:91971650;T:111243138;N:46400,125,125,,,106342222,98049090,91971650,111243138,46400,ERX1497955,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.2785,0.27322,0.08361,0.08291,0.97619,0.97703,0.60537,0.61379,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4361,ERR1427422,ERX1497954,ERS1183256,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#9,SAMEA4012146,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012146|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#9|broker name:ArrayExpress|common name:zebrafish|fsc:24861|gfp:531|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#9|ssc:5852|tissue:Heart|well:A2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#9,LCK 7#9,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 24861:fsc|Experimental Factor: 5852:ssc|Experimental Factor: 531:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_9_mod.bam LCK_7_9.cram,bam cram,,,E MTAB 4617:LCK 7#9,0:125 1:125,A:99732231;C:96455828;G:89233454;T:105851298;N:47439,125,125,,,99732231,96455828,89233454,105851298,47439,ERX1497954,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.21894,0.21406,0.0599,0.05904,0.97861,0.97877,0.57755,0.57546,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4362,ERR1427421,ERX1497953,ERS1183255,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#89,SAMEA4012145,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012145|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#89|broker name:ArrayExpress|common name:zebrafish|fsc:26923|gfp:664|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#89|ssc:7976|tissue:Heart|well:A12,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#89,LCK 7#89,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26923:fsc|Experimental Factor: 7976:ssc|Experimental Factor: 664:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_89_mod.bam LCK_7_89.cram,bam cram,,,E MTAB 4617:LCK 7#89,0:125 1:125,A:53847121;C:51852010;G:47816940;T:57047962;N:23717,125,125,,,53847121,51852010,47816940,57047962,23717,ERX1497953,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22382,0.21939,0.05208,0.05177,0.97952,0.97979,0.49483,0.59346,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4368,ERR1427415,ERX1497947,ERS1183249,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#83,SAMEA4012139,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012139|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#83|broker name:ArrayExpress|common name:zebrafish|fsc:23855|gfp:97|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#83|ssc:7394|tissue:Heart|well:C11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#83,LCK 7#83,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23855:fsc|Experimental Factor: 7394:ssc|Experimental Factor: 97:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_83_mod.bam LCK_7_83.cram,bam cram,,,E MTAB 4617:LCK 7#83,0:125 1:125,A:73686338;C:69380167;G:63301440;T:77949626;N:35429,125,125,,,73686338,69380167,63301440,77949626,35429,ERX1497947,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.1643,0.16094,0.06354,0.06267,0.98526,0.98581,0.60921,0.60841,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4369,ERR1427414,ERX1497946,ERS1183248,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#82,SAMEA4012138,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012138|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#82|broker name:ArrayExpress|common name:zebrafish|fsc:27473|gfp:554|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#82|ssc:9625|tissue:Heart|well:B11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#82,LCK 7#82,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27473:fsc|Experimental Factor: 9625:ssc|Experimental Factor: 554:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_82_mod.bam LCK_7_82.cram,bam cram,,,E MTAB 4617:LCK 7#82,0:125 1:125,A:132306808;C:126337107;G:118115874;T:139760194;N:65267,125,125,,,132306808,126337107,118115874,139760194,65267,ERX1497946,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18655,0.18247,0.05663,0.05588,0.97916,0.97918,0.57019,0.56851,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4370,ERR1427413,ERX1497945,ERS1183247,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#81,SAMEA4012137,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012137|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#81|broker name:ArrayExpress|common name:zebrafish|fsc:26381|gfp:492|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#81|ssc:6369|tissue:Heart|well:A11,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#81,LCK 7#81,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26381:fsc|Experimental Factor: 6369:ssc|Experimental Factor: 492:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_81_mod.bam LCK_7_81.cram,bam cram,,,E MTAB 4617:LCK 7#81,0:125 1:125,A:49752056;C:47569625;G:43787172;T:52848426;N:21471,125,125,,,49752056,47569625,43787172,52848426,21471,ERX1497945,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18831,0.18533,0.05553,0.05564,0.98076,0.98147,0.55231,0.5582,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4377,ERR1427406,ERX1497938,ERS1183240,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#75,SAMEA4012130,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012130|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#75|broker name:ArrayExpress|common name:zebrafish|fsc:29804|gfp:381|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#75|ssc:9855|tissue:Heart|well:C10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#75,LCK 7#75,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 29804:fsc|Experimental Factor: 9855:ssc|Experimental Factor: 381:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_75_mod.bam LCK_7_75.cram,bam cram,,,E MTAB 4617:LCK 7#75,0:125 1:125,A:215270392;C:173814423;G:161953517;T:222035470;N:96448,125,125,,,215270392,173814423,161953517,222035470,96448,ERX1497938,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.40731,0.4045,0.14845,0.14768,0.97908,0.97906,0.59339,0.61288,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4378,ERR1427405,ERX1497937,ERS1183239,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#74,SAMEA4012129,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012129|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:15Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#74|broker name:ArrayExpress|common name:zebrafish|fsc:27947|gfp:352|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#74|ssc:7917|tissue:Heart|well:B10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#74,LCK 7#74,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27947:fsc|Experimental Factor: 7917:ssc|Experimental Factor: 352:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_74_mod.bam LCK_7_74.cram,bam cram,,,E MTAB 4617:LCK 7#74,0:125 1:125,A:123931531;C:111767107;G:106439636;T:128665381;N:58095,125,125,,,123931531,111767107,106439636,128665381,58095,ERX1497937,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.24486,0.2405,0.06375,0.06316,0.97845,0.97938,0.55948,0.55443,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4379,ERR1427404,ERX1497936,ERS1183238,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#73,SAMEA4012128,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012128|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#73|broker name:ArrayExpress|common name:zebrafish|fsc:27976|gfp:511|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#73|ssc:9269|tissue:Heart|well:A10,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#73,LCK 7#73,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27976:fsc|Experimental Factor: 9269:ssc|Experimental Factor: 511:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_73_mod.bam LCK_7_73.cram,bam cram,,,E MTAB 4617:LCK 7#73,0:125 1:125,A:47487658;C:44369011;G:41797745;T:49759850;N:22236,125,125,,,47487658,44369011,41797745,49759850,22236,ERX1497936,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20054,0.19572,0.06216,0.06174,0.98141,0.98165,0.57621,0.56697,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4386,ERR1427397,ERX1497929,ERS1183231,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#67,SAMEA4012121,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012121|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#67|broker name:ArrayExpress|common name:zebrafish|fsc:27129|gfp:522|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#67|ssc:7035|tissue:Heart|well:C9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#67,LCK 7#67,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27129:fsc|Experimental Factor: 7035:ssc|Experimental Factor: 522:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_67_mod.bam LCK_7_67.cram,bam cram,,,E MTAB 4617:LCK 7#67,0:125 1:125,A:211181074;C:167361986;G:152479010;T:214248000;N:87930,125,125,,,211181074,167361986,152479010,214248000,87930,ERX1497929,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.35381,0.35317,0.14449,0.14491,0.97865,0.97897,0.57854,0.58021,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4387,ERR1427396,ERX1497928,ERS1183230,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#66,SAMEA4012120,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012120|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#66|broker name:ArrayExpress|common name:zebrafish|fsc:23015|gfp:48|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#66|ssc:6562|tissue:Heart|well:B9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#66,LCK 7#66,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23015:fsc|Experimental Factor: 6562:ssc|Experimental Factor: 48:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_66_mod.bam LCK_7_66.cram,bam cram,,,E MTAB 4617:LCK 7#66,0:125 1:125,A:122494933;C:109921862;G:103257549;T:125665684;N:56722,125,125,,,122494933,109921862,103257549,125665684,56722,ERX1497928,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.18714,0.18418,0.0608,0.06082,0.9839,0.98441,0.60081,0.59623,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4388,ERR1427395,ERX1497927,ERS1183229,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#65,SAMEA4012119,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012119|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#65|broker name:ArrayExpress|common name:zebrafish|fsc:23857|gfp:308|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#65|ssc:4888|tissue:Heart|well:A9,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#65,LCK 7#65,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23857:fsc|Experimental Factor: 4888:ssc|Experimental Factor: 308:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_65_mod.bam LCK_7_65.cram,bam cram,,,E MTAB 4617:LCK 7#65,0:125 1:125,A:96259909;C:89965165;G:84222055;T:99868995;N:43376,125,125,,,96259909,89965165,84222055,99868995,43376,ERX1497927,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.25582,0.25073,0.07651,0.07583,0.98044,0.98106,0.67809,0.67977,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4395,ERR1427388,ERX1497920,ERS1183222,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#59,SAMEA4012112,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012112|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#59|broker name:ArrayExpress|common name:zebrafish|fsc:20472|gfp:126|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#59|ssc:10300|tissue:Heart|well:C8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#59,LCK 7#59,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 20472:fsc|Experimental Factor: 10300:ssc|Experimental Factor: 126:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_59_mod.bam LCK_7_59.cram,bam cram,,,E MTAB 4617:LCK 7#59,0:125 1:125,A:134247255;C:121203898;G:112067297;T:140566781;N:62269,125,125,,,134247255,121203898,112067297,140566781,62269,ERX1497920,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.27548,0.27103,0.09818,0.09707,0.97861,0.97922,0.54371,0.57755,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4396,ERR1427387,ERX1497919,ERS1183221,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#58,SAMEA4012111,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012111|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#58|broker name:ArrayExpress|common name:zebrafish|fsc:30361|gfp:242|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#58|ssc:7886|tissue:Heart|well:B8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#58,LCK 7#58,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30361:fsc|Experimental Factor: 7886:ssc|Experimental Factor: 242:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_58_mod.bam LCK_7_58.cram,bam cram,,,E MTAB 4617:LCK 7#58,0:125 1:125,A:165043952;C:161634321;G:152303735;T:174314970;N:75022,125,125,,,165043952,161634321,152303735,174314970,75022,ERX1497919,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.16408,0.16208,0.06572,0.06486,0.97918,0.97922,0.52752,0.52567,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4397,ERR1427386,ERX1497918,ERS1183220,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#57,SAMEA4012110,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012110|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#57|broker name:ArrayExpress|common name:zebrafish|fsc:30152|gfp:130|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#57|ssc:6428|tissue:Heart|well:A8,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#57,LCK 7#57,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30152:fsc|Experimental Factor: 6428:ssc|Experimental Factor: 130:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_57_mod.bam LCK_7_57.cram,bam cram,,,E MTAB 4617:LCK 7#57,0:125 1:125,A:81845074;C:82172065;G:76757417;T:87625766;N:38678,125,125,,,81845074,82172065,76757417,87625766,38678,ERX1497918,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.11381,0.11124,0.03217,0.03208,0.98253,0.98299,0.58282,0.58741,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4403,ERR1427380,ERX1497912,ERS1183214,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#51,SAMEA4012104,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012104|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#51|broker name:ArrayExpress|common name:zebrafish|fsc:28503|gfp:536|individual:2|pi:3|plate:7|sample name:E MTAB 4617:LCK 7#51|ssc:5896|tissue:Heart|well:C7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#51,LCK 7#51,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28503:fsc|Experimental Factor: 5896:ssc|Experimental Factor: 536:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_51_mod.bam LCK_7_51.cram,bam cram,,,E MTAB 4617:LCK 7#51,0:125 1:125,A:68083321;C:57560520;G:49834107;T:71348826;N:28226,125,125,,,68083321,57560520,49834107,71348826,28226,ERX1497912,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22734,0.22491,0.09383,0.09424,0.98019,0.98127,0.60101,0.59084,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4404,ERR1427379,ERX1497911,ERS1183213,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#50,SAMEA4012103,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012103|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#50|broker name:ArrayExpress|common name:zebrafish|fsc:27497|gfp:574|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#50|ssc:8308|tissue:Heart|well:B7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#50,LCK 7#50,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27497:fsc|Experimental Factor: 8308:ssc|Experimental Factor: 574:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_50_mod.bam LCK_7_50.cram,bam cram,,,E MTAB 4617:LCK 7#50,0:125 1:125,A:200436684;C:191639110;G:173623845;T:213497904;N:94207,125,125,,,200436684,191639110,173623845,213497904,94207,ERX1497911,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.08784,0.08742,0.04628,0.04599,0.98784,0.98823,0.5655,0.56486,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4406,ERR1427377,ERX1497909,ERS1183211,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#49,SAMEA4012101,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012101|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#49|broker name:ArrayExpress|common name:zebrafish|fsc:30443|gfp:456|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#49|ssc:8077|tissue:Heart|well:A7,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#49,LCK 7#49,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 30443:fsc|Experimental Factor: 8077:ssc|Experimental Factor: 456:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_49_mod.bam LCK_7_49.cram,bam cram,,,E MTAB 4617:LCK 7#49,0:125 1:125,A:96840239;C:94376256;G:85197984;T:104185788;N:45483,125,125,,,96840239,94376256,85197984,104185788,45483,ERX1497909,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.17039,0.16705,0.05666,0.05595,0.98133,0.98196,0.59139,0.59279,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4412,ERR1427371,ERX1497903,ERS1183205,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#43,SAMEA4012095,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012095|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#43|broker name:ArrayExpress|common name:zebrafish|fsc:21270|gfp:120|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#43|ssc:7066|tissue:Heart|well:C6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#43,LCK 7#43,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 21270:fsc|Experimental Factor: 7066:ssc|Experimental Factor: 120:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_43_mod.bam LCK_7_43.cram,bam cram,,,E MTAB 4617:LCK 7#43,0:125 1:125,A:95132366;C:87995738;G:81475905;T:100137372;N:45119,125,125,,,95132366,87995738,81475905,100137372,45119,ERX1497903,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.21518,0.21129,0.06702,0.06612,0.97887,0.97944,0.5799,0.57556,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4413,ERR1427370,ERX1497902,ERS1183204,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#42,SAMEA4012094,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012094|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#42|broker name:ArrayExpress|common name:zebrafish|fsc:19274|gfp:88|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#42|ssc:6422|tissue:Heart|well:B6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#42,LCK 7#42,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 19274:fsc|Experimental Factor: 6422:ssc|Experimental Factor: 88:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_42_mod.bam LCK_7_42.cram,bam cram,,,E MTAB 4617:LCK 7#42,0:125 1:125,A:45015627;C:40505684;G:37787157;T:46787414;N:20618,125,125,,,45015627,40505684,37787157,46787414,20618,ERX1497902,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.14859,0.1471,0.0553,0.05579,0.98058,0.98151,0.57477,0.57968,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4414,ERR1427369,ERX1497901,ERS1183203,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#41,SAMEA4012093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012093|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#41|broker name:ArrayExpress|common name:zebrafish|fsc:20292|gfp:198|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#41|ssc:6233|tissue:Heart|well:A6,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#41,LCK 7#41,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 20292:fsc|Experimental Factor: 6233:ssc|Experimental Factor: 198:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_41_mod.bam LCK_7_41.cram,bam cram,,,E MTAB 4617:LCK 7#41,0:125 1:125,A:89502636;C:89074499;G:83078909;T:95568395;N:39311,125,125,,,89502636,89074499,83078909,95568395,39311,ERX1497901,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.09383,0.09131,0.02199,0.02189,0.98569,0.98577,0.58856,0.59531,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4421,ERR1427362,ERX1497894,ERS1183196,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#35,SAMEA4012086,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012086|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#35|broker name:ArrayExpress|common name:zebrafish|fsc:26079|gfp:93|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#35|ssc:4930|tissue:Heart|well:C5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#35,LCK 7#35,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26079:fsc|Experimental Factor: 4930:ssc|Experimental Factor: 93:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_35_mod.bam LCK_7_35.cram,bam cram,,,E MTAB 4617:LCK 7#35,0:125 1:125,A:139844227;C:137312069;G:126169914;T:149207606;N:69934,125,125,,,139844227,137312069,126169914,149207606,69934,ERX1497894,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.19648,0.19308,0.05501,0.05463,0.98149,0.982,0.60289,0.60804,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4422,ERR1427361,ERX1497893,ERS1183195,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#34,SAMEA4012085,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012085|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#34|broker name:ArrayExpress|common name:zebrafish|fsc:25615|gfp:81|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#34|ssc:5934|tissue:Heart|well:B5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#34,LCK 7#34,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25615:fsc|Experimental Factor: 5934:ssc|Experimental Factor: 81:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_34_mod.bam LCK_7_34.cram,bam cram,,,E MTAB 4617:LCK 7#34,0:125 1:125,A:134481938;C:127574886;G:118538403;T:142102568;N:61455,125,125,,,134481938,127574886,118538403,142102568,61455,ERX1497893,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.19982,0.1964,0.06657,0.0662,0.98092,0.98119,0.59089,0.58445,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4423,ERR1427360,ERX1497892,ERS1183194,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#33,SAMEA4012084,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012084|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#33|broker name:ArrayExpress|common name:zebrafish|fsc:28221|gfp:414|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#33|ssc:5341|tissue:Heart|well:A5,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#33,LCK 7#33,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28221:fsc|Experimental Factor: 5341:ssc|Experimental Factor: 414:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_33_mod.bam LCK_7_33.cram,bam cram,,,E MTAB 4617:LCK 7#33,0:125 1:125,A:93220735;C:94390552;G:86770054;T:100705096;N:43313,125,125,,,93220735,94390552,86770054,100705096,43313,ERX1497892,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.09686,0.09522,0.02902,0.02873,0.98228,0.98279,0.54935,0.54646,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4427,ERR1427356,ERX1497888,ERS1183190,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#3,SAMEA4012080,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012080|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#3|broker name:ArrayExpress|common name:zebrafish|fsc:25075|gfp:108|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#3|ssc:7682|tissue:Heart|well:C1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#3,LCK 7#3,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25075:fsc|Experimental Factor: 7682:ssc|Experimental Factor: 108:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_3_mod.bam LCK_7_3.cram,bam cram,,,E MTAB 4617:LCK 7#3,0:125 1:125,A:58493174;C:54183075;G:50060440;T:61036959;N:28352,125,125,,,58493174,54183075,50060440,61036959,28352,ERX1497888,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.15762,0.1526,0.04924,0.04785,0.97906,0.97966,0.55641,0.55037,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4430,ERR1427353,ERX1497885,ERS1183187,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#27,SAMEA4012077,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012077|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#27|broker name:ArrayExpress|common name:zebrafish|fsc:29359|gfp:456|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#27|ssc:10950|tissue:Heart|well:C4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#27,LCK 7#27,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 29359:fsc|Experimental Factor: 10950:ssc|Experimental Factor: 456:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_27_mod.bam LCK_7_27.cram,bam cram,,,E MTAB 4617:LCK 7#27,0:125 1:125,A:116175271;C:110956295;G:101584573;T:123371066;N:51045,125,125,,,116175271,110956295,101584573,123371066,51045,ERX1497885,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.25865,0.25265,0.08041,0.07902,0.97601,0.97595,0.55457,0.55357,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4431,ERR1427352,ERX1497884,ERS1183186,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#26,SAMEA4012076,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012076|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#26|broker name:ArrayExpress|common name:zebrafish|fsc:25525|gfp:162|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#26|ssc:5861|tissue:Heart|well:B4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#26,LCK 7#26,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 25525:fsc|Experimental Factor: 5861:ssc|Experimental Factor: 162:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_26_mod.bam LCK_7_26.cram,bam cram,,,E MTAB 4617:LCK 7#26,0:125 1:125,A:84022783;C:79751329;G:73366671;T:88820379;N:40588,125,125,,,84022783,79751329,73366671,88820379,40588,ERX1497884,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.13334,0.13062,0.04098,0.04053,0.98405,0.98439,0.43923,0.56542,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4432,ERR1427351,ERX1497883,ERS1183185,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#25,SAMEA4012075,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012075|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#25|broker name:ArrayExpress|common name:zebrafish|fsc:28284|gfp:515|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#25|ssc:8791|tissue:Heart|well:A4,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#25,LCK 7#25,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 28284:fsc|Experimental Factor: 8791:ssc|Experimental Factor: 515:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_25_mod.bam LCK_7_25.cram,bam cram,,,E MTAB 4617:LCK 7#25,0:125 1:125,A:93291373;C:90572911;G:83617400;T:99965116;N:42450,125,125,,,93291373,90572911,83617400,99965116,42450,ERX1497883,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.22059,0.21595,0.06285,0.06239,0.97739,0.97755,0.60441,0.5941,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4438,ERR1427345,ERX1497877,ERS1183179,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#2,SAMEA4012069,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012069|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#2|broker name:ArrayExpress|common name:zebrafish|fsc:26546|gfp:74|individual:2|pi:4|plate:7|sample name:E MTAB 4617:LCK 7#2|ssc:5884|tissue:Heart|well:B1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#2,LCK 7#2,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26546:fsc|Experimental Factor: 5884:ssc|Experimental Factor: 74:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_2_mod.bam LCK_7_2.cram,bam cram,,,E MTAB 4617:LCK 7#2,0:125 1:125,A:50810642;C:45505266;G:42437381;T:52252338;N:22373,125,125,,,50810642,45505266,42437381,52252338,22373,ERX1497877,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.13878,0.13634,0.03454,0.03422,0.98179,0.98238,0.53282,0.54119,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4439,ERR1427344,ERX1497876,ERS1183178,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#19,SAMEA4012068,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012068|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#19|broker name:ArrayExpress|common name:zebrafish|fsc:27939|gfp:269|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#19|ssc:7748|tissue:Heart|well:C3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#19,LCK 7#19,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 27939:fsc|Experimental Factor: 7748:ssc|Experimental Factor: 269:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_19_mod.bam LCK_7_19.cram,bam cram,,,E MTAB 4617:LCK 7#19,0:125 1:125,A:123448577;C:117648440;G:109679332;T:127799152;N:59249,125,125,,,123448577,117648440,109679332,127799152,59249,ERX1497876,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.20997,0.20449,0.04702,0.04606,0.98013,0.98068,0.58105,0.58018,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4440,ERR1427343,ERX1497875,ERS1183177,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#18,SAMEA4012067,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012067|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#18|broker name:ArrayExpress|common name:zebrafish|fsc:23930|gfp:89|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#18|ssc:7002|tissue:Heart|well:B3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#18,LCK 7#18,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23930:fsc|Experimental Factor: 7002:ssc|Experimental Factor: 89:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_18_mod.bam LCK_7_18.cram,bam cram,,,E MTAB 4617:LCK 7#18,0:125 1:125,A:116722795;C:108761302;G:102297772;T:120311653;N:53978,125,125,,,116722795,108761302,102297772,120311653,53978,ERX1497875,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.17035,0.16607,0.04165,0.04071,0.98275,0.98315,0.57334,0.56296,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4441,ERR1427342,ERX1497874,ERS1183176,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#17,SAMEA4012066,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012066|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#17|broker name:ArrayExpress|common name:zebrafish|fsc:19157|gfp:158|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#17|ssc:7404|tissue:Heart|well:A3,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#17,LCK 7#17,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 19157:fsc|Experimental Factor: 7404:ssc|Experimental Factor: 158:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_17_mod.bam LCK_7_17.cram,bam cram,,,E MTAB 4617:LCK 7#17,0:125 1:125,A:114273839;C:106761242;G:100217178;T:118680369;N:52122,125,125,,,114273839,106761242,100217178,118680369,52122,ERX1497874,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.26249,0.25596,0.06917,0.06842,0.9737,0.97425,0.59255,0.59411,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4447,ERR1427336,ERX1497868,ERS1183170,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#11,SAMEA4012060,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012060|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#11|broker name:ArrayExpress|common name:zebrafish|fsc:23053|gfp:148|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#11|ssc:3985|tissue:Heart|well:C2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#11,LCK 7#11,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 23053:fsc|Experimental Factor: 3985:ssc|Experimental Factor: 148:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_11_mod.bam LCK_7_11.cram,bam cram,,,E MTAB 4617:LCK 7#11,0:125 1:125,A:94603298;C:90252097;G:83046109;T:99899414;N:44332,125,125,,,94603298,90252097,83046109,99899414,44332,ERX1497868,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.24988,0.24291,0.07669,0.07453,0.97857,0.97901,0.52877,0.53451,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4448,ERR1427335,ERX1497867,ERS1183169,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#10,SAMEA4012059,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012059|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#10|broker name:ArrayExpress|common name:zebrafish|fsc:26350|gfp:91|individual:2|pi:2|plate:7|sample name:E MTAB 4617:LCK 7#10|ssc:5717|tissue:Heart|well:B2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#10,LCK 7#10,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 26350:fsc|Experimental Factor: 5717:ssc|Experimental Factor: 91:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_10_mod.bam LCK_7_10.cram,bam cram,,,E MTAB 4617:LCK 7#10,0:125 1:125,A:136048498;C:130651014;G:121379521;T:142822578;N:64889,125,125,,,136048498,130651014,121379521,142822578,64889,ERX1497867,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.14978,0.14551,0.04586,0.0445,0.98516,0.98559,0.55716,0.54592,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
4449,ERR1427334,ERX1497866,ERS1183168,ERP015799,PRJEB14175,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E-MTAB-4617,Transcriptome Analysis,Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP  forward and side light scatter and dead cell staining,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617,,Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,LCK 7#1,SAMEA4012058,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics",ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012058|INSDC center alias:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research  University of Lausanne  Lausanne  Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#1|broker name:ArrayExpress|common name:zebrafish|fsc:22006|gfp:487|individual:2|pi:1|plate:7|sample name:E MTAB 4617:LCK 7#1|ssc:6542|tissue:Heart|well:A1,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,E MTAB 4617:LCK 7#1,LCK 7#1,Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted  using a Becton Dickinson Influx sorter with 488  and 561 nm lasers Schulte et al.  2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size  granularity and level of fluorescence for each cell were simultaneously recorded.  The Smart seq2 protocol Picelli et al.  2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.,Experimental Factor: Heart:tissue|Experimental Factor: 22006:fsc|Experimental Factor: 6542:ssc|Experimental Factor: 487:gfp,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP015799,Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish,ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16,LCK_7_1_mod.bam LCK_7_1.cram,bam cram,,,E MTAB 4617:LCK 7#1,0:125 1:125,A:128250593;C:122748202;G:114418508;T:135400263;N:59934,125,125,,,128250593,122748202,114418508,135400263,59934,ERX1497866,,ERA631093,"Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive","Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive",2,0.15168,0.14994,0.07129,0.07092,0.98202,0.98163,0.61662,0.63065,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,sc,single_cell_plate,smartseq,,Switzerland,2016-05-26,Adult,Adult,Heart,Cardiovascular System
49899,SRR8883780,SRX5669581,SRS4612450,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,148 2 E12 KOcxcl12a 6,GSM3719008,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,148 2 E12 KOcxcl12a 6,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719008,GSM3719008: 148 2 E12 KOcxcl12a 6; Danio rerio; RNA Seq,GSM3719008,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719008,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,148-2-E12-KOcxcl12a-6_all_lanes_R1.fastq.gz 148-2-E12-KOcxcl12a-6_all_lanes_R2.fastq.gz,fastq fastq,99264702.0,667893.0,GSM3719008 r1,0:74.31 1:74.31,A:24182760;C:25303406;G:25958104;T:23740781;N:79651,74,74,,,24182760,25303406,25958104,23740781,79651,SRX5669581,SRS4612450,SRA798477,GEO,University of Oxford,2,0.91963,0.91707,0.25543,0.25598,0.77885,0.78526,0.64562,0.65202,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49900,SRR8883779,SRX5669580,SRS4612449,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,147 2 E11 KOcxcl12a 5,GSM3719007,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,147 2 E11 KOcxcl12a 5,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719007,GSM3719007: 147 2 E11 KOcxcl12a 5; Danio rerio; RNA Seq,GSM3719007,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719007,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,147-2-E11-KOcxcl12a-5_all_lanes_R2.fastq.gz 147-2-E11-KOcxcl12a-5_all_lanes_R1.fastq.gz,fastq fastq,106939236.0,718050.0,GSM3719007 r1,0:74.47 1:74.47,A:25999817;C:27345657;G:27993944;T:25531888;N:67930,74,74,,,25999817,27345657,27993944,25531888,67930,SRX5669580,SRS4612449,SRA798477,GEO,University of Oxford,2,0.93397,0.9304,0.28472,0.28391,0.78995,0.79377,0.63586,0.63708,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49901,SRR8883778,SRX5669579,SRS4612448,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,146 2 E10 KOcxcl12a 4,GSM3719006,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,146 2 E10 KOcxcl12a 4,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719006,GSM3719006: 146 2 E10 KOcxcl12a 4; Danio rerio; RNA Seq,GSM3719006,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719006,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,146-2-E10-KOcxcl12a-4_all_lanes_R2.fastq.gz 146-2-E10-KOcxcl12a-4_all_lanes_R1.fastq.gz,fastq fastq,128269313.0,868280.0,GSM3719006 r1,0:73.86 1:73.86,A:31007547;C:32979513;G:33717602;T:30425592;N:139059,73,73,,,31007547,32979513,33717602,30425592,139059,SRX5669579,SRS4612448,SRA798477,GEO,University of Oxford,2,0.92669,0.92674,0.24854,0.24879,0.78727,0.79164,0.64818,0.65414,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49902,SRR8883777,SRX5669578,SRS4612447,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,145 2 E09 KOcxcl12a 3,GSM3719005,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,145 2 E09 KOcxcl12a 3,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719005,GSM3719005: 145 2 E09 KOcxcl12a 3; Danio rerio; RNA Seq,GSM3719005,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719005,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,145-2-E09-KOcxcl12a-3_all_lanes_R1.fastq.gz 145-2-E09-KOcxcl12a-3_all_lanes_R2.fastq.gz,fastq fastq,121755625.0,825242.0,GSM3719005 r1,0:73.77 1:73.77,A:30614648;C:30136581;G:30787289;T:30068959;N:148148,73,73,,,30614648,30136581,30787289,30068959,148148,SRX5669578,SRS4612447,SRA798477,GEO,University of Oxford,2,0.91445,0.91357,0.3015,0.30027,0.7781,0.78186,0.63683,0.63951,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49903,SRR8883776,SRX5669577,SRS4612446,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,144 2 E08 KOcxcl12a 2,GSM3719004,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,144 2 E08 KOcxcl12a 2,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719004,GSM3719004: 144 2 E08 KOcxcl12a 2; Danio rerio; RNA Seq,GSM3719004,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719004,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,144-2-E08-KOcxcl12a-2_all_lanes_R1.fastq.gz 144-2-E08-KOcxcl12a-2_all_lanes_R2.fastq.gz,fastq fastq,109985812.0,742694.0,GSM3719004 r1,0:74.04 1:74.05,A:26580402;C:28348797;G:28922104;T:26031320;N:103189,74,74,,,26580402,28348797,28922104,26031320,103189,SRX5669577,SRS4612446,SRA798477,GEO,University of Oxford,2,0.93276,0.93175,0.25341,0.25219,0.78141,0.78405,0.65277,0.65585,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49904,SRR8883775,SRX5669576,SRS4612445,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,143 2 E07 KOcxcl12a 1,GSM3719003,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,143 2 E07 KOcxcl12a 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719003,GSM3719003: 143 2 E07 KOcxcl12a 1; Danio rerio; RNA Seq,GSM3719003,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719003,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,143-2-E07-KOcxcl12a-1_all_lanes_R1.fastq.gz 143-2-E07-KOcxcl12a-1_all_lanes_R2.fastq.gz,fastq fastq,94811811.0,636658.0,GSM3719003 r1,0:74.46 1:74.46,A:22658972;C:24643435;G:25238963;T:22205729;N:64712,74,74,,,22658972,24643435,25238963,22205729,64712,SRX5669576,SRS4612445,SRA798477,GEO,University of Oxford,2,0.92745,0.92691,0.23249,0.23126,0.78658,0.79076,0.64976,0.63056,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49905,SRR8883774,SRX5669575,SRS4612444,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,142 2 E06 KOcxcl12a ctr 3,GSM3719002,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,142 2 E06 KOcxcl12a ctr 3,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719002,GSM3719002: 142 2 E06 KOcxcl12a ctr 3; Danio rerio; RNA Seq,GSM3719002,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719002,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,142-2-E06-KOcxcl12a-ctr-3_all_lanes_R1.fastq.gz 142-2-E06-KOcxcl12a-ctr-3_all_lanes_R2.fastq.gz,fastq fastq,129809456.0,880087.0,GSM3719002 r1,0:73.75 1:73.75,A:30887867;C:33831790;G:34633569;T:30274300;N:181930,73,73,,,30887867,33831790,34633569,30274300,181930,SRX5669575,SRS4612444,SRA798477,GEO,University of Oxford,2,0.92838,0.92684,0.2376,0.23787,0.78636,0.79115,0.65598,0.63686,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49906,SRR8883773,SRX5669574,SRS4612443,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,141 2 E05 KOcxcl12a ctr 2,GSM3719001,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,141 2 E05 KOcxcl12a ctr 2,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719001,GSM3719001: 141 2 E05 KOcxcl12a ctr 2; Danio rerio; RNA Seq,GSM3719001,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719001,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,141-2-E05-KOcxcl12a-ctr-2_all_lanes_R1.fastq.gz 141-2-E05-KOcxcl12a-ctr-2_all_lanes_R2.fastq.gz,fastq fastq,107380357.0,726760.0,GSM3719001 r1,0:73.87 1:73.88,A:26228066;C:27324290;G:27986915;T:25712036;N:129050,73,73,,,26228066,27324290,27986915,25712036,129050,SRX5669574,SRS4612443,SRA798477,GEO,University of Oxford,2,0.91412,0.91386,0.22813,0.22895,0.77784,0.78362,0.63341,0.63642,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49907,SRR8883772,SRX5669573,SRS4612442,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,140 2 E04 KOcxcl12a ctr 1,GSM3719000,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,140 2 E04 KOcxcl12a ctr 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3719000,GSM3719000: 140 2 E04 KOcxcl12a ctr 1; Danio rerio; RNA Seq,GSM3719000,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3719000,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,140-2-E04-KOcxcl12a-ctr-1_all_lanes_R1.fastq.gz 140-2-E04-KOcxcl12a-ctr-1_all_lanes_R2.fastq.gz,fastq fastq,108418608.0,731612.0,GSM3719000 r1,0:74.10 1:74.09,A:26582166;C:27511188;G:28160622;T:26054265;N:110367,74,74,,,26582166,27511188,28160622,26054265,110367,SRX5669573,SRS4612442,SRA798477,GEO,University of Oxford,2,0.9189,0.91754,0.23947,0.23587,0.78084,0.78522,0.64092,0.59963,75,73,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49908,SRR8883771,SRX5669572,SRS4612441,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,139 2 E03 KOtgm2b 6,GSM3718999,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,139 2 E03 KOtgm2b 6,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718999,GSM3718999: 139 2 E03 KOtgm2b 6; Danio rerio; RNA Seq,GSM3718999,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718999,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,139-2-E03-KOtgm2b-6_all_lanes_R1.fastq.gz 139-2-E03-KOtgm2b-6_all_lanes_R2.fastq.gz,fastq fastq,109962833.0,738854.0,GSM3718999 r1,0:74.41 1:74.42,A:26858777;C:28073839;G:28708123;T:26241362;N:80732,74,74,,,26858777,28073839,28708123,26241362,80732,SRX5669572,SRS4612441,SRA798477,GEO,University of Oxford,2,0.9353,0.93342,0.19619,0.19724,0.754,0.75607,0.60298,0.60929,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49909,SRR8883770,SRX5669571,SRS4612440,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,138 2 E02 KOtgm2b 5,GSM3718998,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,138 2 E02 KOtgm2b 5,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718998,GSM3718998: 138 2 E02 KOtgm2b 5; Danio rerio; RNA Seq,GSM3718998,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718998,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,138-2-E02-KOtgm2b-5_all_lanes_R1.fastq.gz 138-2-E02-KOtgm2b-5_all_lanes_R2.fastq.gz,fastq fastq,100462360.0,671960.0,GSM3718998 r1,0:74.75 1:74.75,A:24544858;C:25599584;G:26221724;T:24054453;N:41741,74,74,,,24544858,25599584,26221724,24054453,41741,SRX5669571,SRS4612440,SRA798477,GEO,University of Oxford,2,0.94446,0.94375,0.19662,0.19723,0.75124,0.75588,0.58577,0.56794,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49910,SRR8883769,SRX5669570,SRS4612439,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,137 2 E01 KOtgm2b 4,GSM3718997,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,137 2 E01 KOtgm2b 4,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718997,GSM3718997: 137 2 E01 KOtgm2b 4; Danio rerio; RNA Seq,GSM3718997,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718997,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,137-2-E01-KOtgm2b-4_all_lanes_R1.fastq.gz 137-2-E01-KOtgm2b-4_all_lanes_R2.fastq.gz,fastq fastq,106854841.0,717396.0,GSM3718997 r1,0:74.47 1:74.47,A:25509330;C:27879859;G:28531018;T:24874276;N:60358,74,74,,,25509330,27879859,28531018,24874276,60358,SRX5669570,SRS4612439,SRA798477,GEO,University of Oxford,2,0.92486,0.92304,0.21065,0.21002,0.77275,0.7777,0.63212,0.63504,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49911,SRR8883768,SRX5669569,SRS4612438,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,136 2 D12 KOtgm2b 3,GSM3718996,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,136 2 D12 KOtgm2b 3,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718996,GSM3718996: 136 2 D12 KOtgm2b 3; Danio rerio; RNA Seq,GSM3718996,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718996,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,136-2-D12-KOtgm2b-3_all_lanes_R1.fastq.gz 136-2-D12-KOtgm2b-3_all_lanes_R2.fastq.gz,fastq fastq,92141370.0,620781.0,GSM3718996 r1,0:74.21 1:74.22,A:23141972;C:22908175;G:23441104;T:22555763;N:94356,74,74,,,23141972,22908175,23441104,22555763,94356,SRX5669569,SRS4612438,SRA798477,GEO,University of Oxford,2,0.92674,0.92438,0.19612,0.19794,0.74854,0.75755,0.55401,0.56341,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49912,SRR8883767,SRX5669568,SRS4612437,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,135 2 D11 KOtgm2b 2,GSM3718995,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,135 2 D11 KOtgm2b 2,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718995,GSM3718995: 135 2 D11 KOtgm2b 2; Danio rerio; RNA Seq,GSM3718995,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718995,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,135-2-D11-KOtgm2b-2_all_lanes_R1.fastq.gz 135-2-D11-KOtgm2b-2_all_lanes_R2.fastq.gz,fastq fastq,66274479.0,443320.0,GSM3718995 r1,0:74.74 1:74.75,A:16243668;C:16886199;G:17301289;T:15810059;N:33264,74,74,,,16243668,16886199,17301289,15810059,33264,SRX5669568,SRS4612437,SRA798477,GEO,University of Oxford,2,0.93842,0.93704,0.22403,0.22571,0.7643,0.77218,0.62341,0.62445,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49913,SRR8883766,SRX5669567,SRS4612436,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,134 2 D10 KOtgm2b 1,GSM3718994,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,134 2 D10 KOtgm2b 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718994,GSM3718994: 134 2 D10 KOtgm2b 1; Danio rerio; RNA Seq,GSM3718994,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718994,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,134-2-D10-KOtgm2b-1_all_lanes_R1.fastq.gz 134-2-D10-KOtgm2b-1_all_lanes_R2.fastq.gz,fastq fastq,60384203.0,405320.0,GSM3718994 r1,0:74.48 1:74.50,A:15095234;C:15063807;G:15456958;T:14724791;N:43413,74,74,,,15095234,15063807,15456958,14724791,43413,SRX5669567,SRS4612436,SRA798477,GEO,University of Oxford,2,0.92886,0.92692,0.21819,0.21631,0.7525,0.76077,0.53347,0.50585,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49914,SRR8883765,SRX5669566,SRS4612435,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,133 2 D09 KOtgm2b ctr 3,GSM3718993,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,133 2 D09 KOtgm2b ctr 3,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718993,GSM3718993: 133 2 D09 KOtgm2b ctr 3; Danio rerio; RNA Seq,GSM3718993,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718993,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,133-2-D09-KOtgm2b-ctr-3_all_lanes_R1.fastq.gz 133-2-D09-KOtgm2b-ctr-3_all_lanes_R2.fastq.gz,fastq fastq,48591328.0,327743.0,GSM3718993 r1,0:74.13 1:74.13,A:12088250;C:12179083;G:12474240;T:11798218;N:51537,74,74,,,12088250,12179083,12474240,11798218,51537,SRX5669566,SRS4612435,SRA798477,GEO,University of Oxford,2,0.9338,0.93207,0.21936,0.22034,0.76359,0.76948,0.60676,0.59959,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49915,SRR8883764,SRX5669565,SRS4612434,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,132 2 D08 KOtgm2b ctr 2,GSM3718992,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,132 2 D08 KOtgm2b ctr 2,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718992,GSM3718992: 132 2 D08 KOtgm2b ctr 2; Danio rerio; RNA Seq,GSM3718992,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718992,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,132-2-D08-KOtgm2b-ctr-2_all_lanes_R1.fastq.gz 132-2-D08-KOtgm2b-ctr-2_all_lanes_R2.fastq.gz,fastq fastq,49669187.0,334909.0,GSM3718992 r1,0:74.15 1:74.16,A:12028296;C:12782564;G:13085690;T:11722181;N:50456,74,74,,,12028296,12782564,13085690,11722181,50456,SRX5669565,SRS4612434,SRA798477,GEO,University of Oxford,2,0.93318,0.93238,0.21044,0.21218,0.76952,0.7783,0.62232,0.6203,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49916,SRR8883763,SRX5669564,SRS4612433,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,131 2 D07 KOtgm2b ctr 1,GSM3718991,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,131 2 D07 KOtgm2b ctr 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718991,GSM3718991: 131 2 D07 KOtgm2b ctr 1; Danio rerio; RNA Seq,GSM3718991,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718991,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,131-2-D07-KOtgm2b-ctr-1_all_lanes_R1.fastq.gz 131-2-D07-KOtgm2b-ctr-1_all_lanes_R2.fastq.gz,fastq fastq,54297432.0,364230.0,GSM3718991 r1,0:74.54 1:74.54,A:13104680;C:14014488;G:14341190;T:12803752;N:33322,74,74,,,13104680,14014488,14341190,12803752,33322,SRX5669564,SRS4612433,SRA798477,GEO,University of Oxford,2,0.93946,0.94013,0.2414,0.23899,0.77674,0.78344,0.64098,0.61967,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49917,SRR8883762,SRX5669563,SRS4612432,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,130 2 D06 KOsema3fb tbx18 1,GSM3718990,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,130 2 D06 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718990,GSM3718990: 130 2 D06 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718990,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718990,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,130-2-D06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 130-2-D06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,110234157.0,747392.0,GSM3718990 r1,0:73.74 1:73.76,A:28431221;C:26396031;G:27503562;T:27711266;N:192077,73,73,,,28431221,26396031,27503562,27711266,192077,SRX5669563,SRS4612432,SRA798477,GEO,University of Oxford,2,0.77713,0.76755,0.25874,0.25566,0.99117,0.99105,0.84401,0.71613,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49918,SRR8883761,SRX5669562,SRS4612431,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,129 2 D05 KOsema3fb tbx18 1,GSM3718989,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,129 2 D05 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718989,GSM3718989: 129 2 D05 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718989,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718989,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,129-2-D05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 129-2-D05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,72776114.0,491364.0,GSM3718989 r1,0:74.05 1:74.06,A:18647181;C:17661907;G:18133434;T:18240577;N:93015,74,74,,,18647181,17661907,18133434,18240577,93015,SRX5669562,SRS4612431,SRA798477,GEO,University of Oxford,2,0.83344,0.82903,0.1213,0.12432,0.97388,0.9739,0.64406,0.65393,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49919,SRR8883760,SRX5669561,SRS4612430,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,128 2 D04 KOsema3fb tbx18 1,GSM3718988,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,128 2 D04 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718988,GSM3718988: 128 2 D04 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718988,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,128-2-D04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 128-2-D04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,91788863.0,616504.0,GSM3718988 r1,0:74.44 1:74.45,A:25144004;C:20519360;G:21226945;T:24818679;N:79875,74,74,,,25144004,20519360,21226945,24818679,79875,SRX5669561,SRS4612430,SRA798477,GEO,University of Oxford,2,0.8087,0.80627,0.34661,0.34232,0.95763,0.95832,0.61953,0.64507,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49920,SRR8883759,SRX5669560,SRS4612429,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,127 2 D03 KOsema3fb tbx18 1,GSM3718987,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,127 2 D03 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718987,GSM3718987: 127 2 D03 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718987,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,127-2-D03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 127-2-D03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,99060843.0,665407.0,GSM3718987 r1,0:74.43 1:74.44,A:26599641;C:22804504;G:23489807;T:26082542;N:84349,74,74,,,26599641,22804504,23489807,26082542,84349,SRX5669560,SRS4612429,SRA798477,GEO,University of Oxford,2,0.84494,0.84083,0.34251,0.3408,0.94846,0.94931,0.61735,0.62618,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49921,SRR8883758,SRX5669559,SRS4612428,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,126 2 D02 KOsema3fb tbx18 1,GSM3718986,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,126 2 D02 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718986,GSM3718986: 126 2 D02 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718986,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718986,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,126-2-D02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 126-2-D02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,89497403.0,599998.0,GSM3718986 r1,0:74.58 1:74.58,A:23556468;C:21386062;G:21724809;T:22782097;N:47967,74,74,,,23556468,21386062,21724809,22782097,47967,SRX5669559,SRS4612428,SRA798477,GEO,University of Oxford,2,0.90048,0.90027,0.08906,0.09149,0.95136,0.95187,0.68687,0.69086,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49922,SRR8883757,SRX5669558,SRS4612427,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,125 2 D01 KOsema3fb tbx18 1,GSM3718985,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,125 2 D01 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718985,GSM3718985: 125 2 D01 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718985,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718985,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,125-2-D01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 125-2-D01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,48185478.0,321734.0,GSM3718985 r1,0:74.88 1:74.89,A:12090976;C:12002728;G:12234353;T:11829653;N:27768,74,74,,,12090976,12002728,12234353,11829653,27768,SRX5669558,SRS4612427,SRA798477,GEO,University of Oxford,2,0.84457,0.84125,0.13895,0.13881,0.96625,0.96674,0.58767,0.58139,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49923,SRR8883756,SRX5669557,SRS4612426,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,124 2 C12 KOsema3fb tbx18 1,GSM3718984,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,124 2 C12 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718984,GSM3718984: 124 2 C12 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718984,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718984,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,124-2-C12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 124-2-C12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,135607116.0,915406.0,GSM3718984 r1,0:74.07 1:74.07,A:32159235;C:34890150;G:36630005;T:31695707;N:232019,74,74,,,32159235,34890150,36630005,31695707,232019,SRX5669557,SRS4612426,SRA798477,GEO,University of Oxford,2,0.76677,0.75662,0.2656,0.26203,0.99492,0.99523,0.63635,0.65929,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49924,SRR8883755,SRX5669556,SRS4612425,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,123 2 C11 KOsema3fb tbx18 1,GSM3718983,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,123 2 C11 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718983,GSM3718983: 123 2 C11 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718983,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718983,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,123-2-C11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 123-2-C11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,87497086.0,587638.0,GSM3718983 r1,0:74.45 1:74.45,A:23448862;C:20175987;G:21185040;T:22585978;N:101219,74,74,,,23448862,20175987,21185040,22585978,101219,SRX5669556,SRS4612425,SRA798477,GEO,University of Oxford,2,0.82255,0.81241,0.12138,0.12127,0.99711,0.99711,0.9386,0.93959,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49925,SRR8883754,SRX5669555,SRS4612424,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,122 2 C10 KOsema3fb tbx18 1,GSM3718982,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,122 2 C10 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718982,GSM3718982: 122 2 C10 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718982,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718982,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,122-2-C10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 122-2-C10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,62517978.0,418828.0,GSM3718982 r1,0:74.64 1:74.63,A:16436794;C:14921072;G:15287825;T:15822124;N:50163,74,74,,,16436794,14921072,15287825,15822124,50163,SRX5669555,SRS4612424,SRA798477,GEO,University of Oxford,2,0.87516,0.87101,0.05328,0.05476,0.9514,0.95138,0.57772,0.62333,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49926,SRR8883753,SRX5669554,SRS4612423,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,121 2 C09 KOsema3fb tbx18 1,GSM3718981,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,121 2 C09 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718981,GSM3718981: 121 2 C09 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718981,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718981,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,121-2-C09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 121-2-C09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,136153223.0,922773.0,GSM3718981 r1,0:73.77 1:73.77,A:37426170;C:30362404;G:31332794;T:36834225;N:197630,73,73,,,37426170,30362404,31332794,36834225,197630,SRX5669554,SRS4612423,SRA798477,GEO,University of Oxford,2,0.84938,0.84505,0.17896,0.18056,0.92427,0.92441,0.60599,0.59117,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49927,SRR8883752,SRX5669553,SRS4612422,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,120 2 C08 KOsema3fb tbx18 1,GSM3718980,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,120 2 C08 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718980,GSM3718980: 120 2 C08 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718980,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718980,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,120-2-C08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 120-2-C08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,111876800.0,754706.0,GSM3718980 r1,0:74.12 1:74.12,A:29690879;C:25910779;G:26899072;T:29225413;N:150657,74,74,,,29690879,25910779,26899072,29225413,150657,SRX5669553,SRS4612422,SRA798477,GEO,University of Oxford,2,0.78833,0.78334,0.38511,0.382,0.96924,0.9694,0.68874,0.68759,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49928,SRR8883744,SRX5669552,SRS4612421,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,119 2 C07 KOsema3fb tbx18 1,GSM3718979,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,119 2 C07 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718979,GSM3718979: 119 2 C07 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718979,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718979,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,119-2-C07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 119-2-C07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,156489712.0,1053300.0,GSM3718979 r1,0:74.29 1:74.28,A:45673694;C:32030116;G:33486582;T:45151963;N:147357,74,74,,,45673694,32030116,33486582,45151963,147357,SRX5669552,SRS4612421,SRA798477,GEO,University of Oxford,2,0.815,0.80967,0.35748,0.354,0.98031,0.98015,0.92183,0.91637,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49929,SRR8883743,SRX5669551,SRS4612420,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,118 2 C06 KOsema3fb tbx18 1,GSM3718978,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,118 2 C06 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718978,GSM3718978: 118 2 C06 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718978,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718978,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,118-2-C06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 118-2-C06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,97946060.0,657322.0,GSM3718978 r1,0:74.50 1:74.51,A:28975729;C:19954414;G:20745385;T:28174552;N:95980,74,74,,,28975729,19954414,20745385,28174552,95980,SRX5669551,SRS4612420,SRA798477,GEO,University of Oxford,2,0.88899,0.88117,0.01232,0.01239,0.99823,0.99825,0.82129,0.81747,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49930,SRR8883742,SRX5669550,SRS4612419,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,117 2 C05 KOsema3fb tbx18 1,GSM3718977,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,117 2 C05 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718977,GSM3718977: 117 2 C05 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718977,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718977,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,117-2-C05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 117-2-C05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,69214846.0,465753.0,GSM3718977 r1,0:74.30 1:74.31,A:18761059;C:15617433;G:16216548;T:18532653;N:87153,74,74,,,18761059,15617433,16216548,18532653,87153,SRX5669550,SRS4612419,SRA798477,GEO,University of Oxford,2,0.76854,0.76093,0.15615,0.15563,0.93066,0.93119,0.58239,0.60187,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49931,SRR8883741,SRX5669549,SRS4612418,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,116 2 C04 KOsema3fb tbx18 1,GSM3718976,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,116 2 C04 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718976,GSM3718976: 116 2 C04 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718976,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718976,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,116-2-C04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 116-2-C04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,75472427.0,507600.0,GSM3718976 r1,0:74.34 1:74.34,A:20859539;C:16681986;G:17258567;T:20586679;N:85656,74,74,,,20859539,16681986,17258567,20586679,85656,SRX5669549,SRS4612418,SRA798477,GEO,University of Oxford,2,0.81342,0.80704,0.26123,0.25994,0.9347,0.93464,0.54291,0.54243,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49932,SRR8883740,SRX5669548,SRS4612417,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,115 2 C03 KOsema3fb tbx18 1,GSM3718975,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,115 2 C03 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718975,GSM3718975: 115 2 C03 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718975,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718975,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,115-2-C03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 115-2-C03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,82962806.0,556564.0,GSM3718975 r1,0:74.53 1:74.53,A:23001088;C:18396897;G:18830206;T:22674040;N:60575,74,74,,,23001088,18396897,18830206,22674040,60575,SRX5669548,SRS4612417,SRA798477,GEO,University of Oxford,2,0.89917,0.89649,0.161,0.16093,0.92443,0.92468,0.59905,0.60072,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49933,SRR8883739,SRX5669547,SRS4612416,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,114 2 C02 KOsema3fb tbx18 1,GSM3718974,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,114 2 C02 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718974,GSM3718974: 114 2 C02 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718974,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718974,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,114-2-C02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 114-2-C02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,106216907.0,712267.0,GSM3718974 r1,0:74.56 1:74.56,A:29174324;C:23794193;G:24434136;T:28754518;N:59736,74,74,,,29174324,23794193,24434136,28754518,59736,SRX5669547,SRS4612416,SRA798477,GEO,University of Oxford,2,0.90487,0.90038,0.29101,0.29055,0.88176,0.88258,0.55682,0.55632,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49934,SRR8883738,SRX5669546,SRS4612415,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,113 2 C01 KOsema3fb tbx18 1,GSM3718973,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,113 2 C01 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718973,GSM3718973: 113 2 C01 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718973,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718973,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,113-2-C01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 113-2-C01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,131443192.0,885217.0,GSM3718973 r1,0:74.24 1:74.24,A:33392659;C:31910928;G:33134031;T:32853539;N:152035,74,74,,,33392659,31910928,33134031,32853539,152035,SRX5669546,SRS4612415,SRA798477,GEO,University of Oxford,2,0.76875,0.763,0.34113,0.33651,0.98236,0.98238,0.7352,0.71836,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49935,SRR8883737,SRX5669545,SRS4612414,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,112 2 B12 KOsema3fb tbx18 1,GSM3718972,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,112 2 B12 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718972,GSM3718972: 112 2 B12 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718972,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718972,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,112-2-B12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 112-2-B12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,75374963.0,504536.0,GSM3718972 r1,0:74.69 1:74.70,A:19871639;C:17630596;G:18334709;T:19474458;N:63561,74,74,,,19871639,17630596,18334709,19474458,63561,SRX5669545,SRS4612414,SRA798477,GEO,University of Oxford,2,0.79501,0.78698,0.31679,0.31493,0.97126,0.97161,0.69061,0.68695,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49936,SRR8883736,SRX5669544,SRS4612413,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,111 2 B11 KOsema3fb tbx18 1,GSM3718971,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,111 2 B11 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718971,GSM3718971: 111 2 B11 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718971,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718971,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,111-2-B11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 111-2-B11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,61306141.0,409447.0,GSM3718971 r1,0:74.86 1:74.87,A:17078666;C:13397099;G:14017031;T:16767954;N:45391,74,74,,,17078666,13397099,14017031,16767954,45391,SRX5669544,SRS4612413,SRA798477,GEO,University of Oxford,2,0.78279,0.77063,0.29509,0.2912,0.94943,0.94972,0.68066,0.66888,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49937,SRR8883735,SRX5669543,SRS4612412,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,110 2 B09 KOsema3fb tbx18 1,GSM3718970,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,110 2 B09 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718970,GSM3718970: 110 2 B09 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718970,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718970,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,110-2-B09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 110-2-B09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,77611492.0,517973.0,GSM3718970 r1,0:74.92 1:74.92,A:20828796;C:18000975;G:18473556;T:20273490;N:34675,74,74,,,20828796,18000975,18473556,20273490,34675,SRX5669543,SRS4612412,SRA798477,GEO,University of Oxford,2,0.8943,0.8898,0.07119,0.07297,0.96376,0.96376,0.65962,0.66776,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49938,SRR8883734,SRX5669542,SRS4612411,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,109 2 B08 KOsema3fb tbx18 1,GSM3718969,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,109 2 B08 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718969,GSM3718969: 109 2 B08 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718969,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718969,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,109-2-B08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 109-2-B08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,129418006.0,863669.0,GSM3718969 r1,0:74.92 1:74.92,A:38739420;C:25964234;G:27042729;T:37614526;N:57097,74,74,,,38739420,25964234,27042729,37614526,57097,SRX5669542,SRS4612411,SRA798477,GEO,University of Oxford,2,0.90082,0.89259,0.10991,0.10917,0.99383,0.99371,0.98678,0.98259,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49939,SRR8883733,SRX5669541,SRS4612410,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,108 2 B07 KOsema3fb tbx18 1,GSM3718968,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,108 2 B07 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718968,GSM3718968: 108 2 B07 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718968,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718968,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,108-2-B07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 108-2-B07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,64293554.0,427843.0,GSM3718968 r1,0:75.14 1:75.14,A:16371370;C:15659136;G:16037461;T:16204914;N:20673,75,75,,,16371370,15659136,16037461,16204914,20673,SRX5669541,SRS4612410,SRA798477,GEO,University of Oxford,2,0.88538,0.88147,0.09713,0.10128,0.96408,0.96414,0.57841,0.57128,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49940,SRR8883732,SRX5669540,SRS4612409,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,107 2 B06 KOsema3fb tbx18 1,GSM3718967,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,107 2 B06 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718967,GSM3718967: 107 2 B06 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718967,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718967,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,107-2-B06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 107-2-B06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,87019759.0,578810.0,GSM3718967 r1,0:75.17 1:75.17,A:24569329;C:18725958;G:19314464;T:24386952;N:23056,75,75,,,24569329,18725958,19314464,24386952,23056,SRX5669540,SRS4612409,SRA798477,GEO,University of Oxford,2,0.88053,0.87769,0.22651,0.22723,0.93103,0.93178,0.6335,0.54178,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49941,SRR8883731,SRX5669539,SRS4612408,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,106 2 B05 KOsema3fb tbx18 1,GSM3718966,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,106 2 B05 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718966,GSM3718966: 106 2 B05 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718966,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718966,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,106-2-B05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 106-2-B05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,171458105.0,1143747.0,GSM3718966 r1,0:74.95 1:74.96,A:46877212;C:38285761;G:39836533;T:46388650;N:69949,74,74,,,46877212,38285761,39836533,46388650,69949,SRX5669539,SRS4612408,SRA798477,GEO,University of Oxford,2,0.8191,0.81279,0.43731,0.43052,0.98397,0.98533,0.83233,0.63073,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49942,SRR8883730,SRX5669538,SRS4612407,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,105 2 B04 KOsema3fb tbx18 1,GSM3718965,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,105 2 B04 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718965,GSM3718965: 105 2 B04 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718965,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718965,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,105-2-B04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 105-2-B04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,127662981.0,854443.0,GSM3718965 r1,0:74.70 1:74.71,A:29584063;C:34031538;G:35345753;T:28597787;N:103840,74,74,,,29584063,34031538,35345753,28597787,103840,SRX5669538,SRS4612407,SRA798477,GEO,University of Oxford,2,0.68467,0.67957,0.25187,0.2499,0.99502,0.99502,0.7152,0.71768,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49943,SRR8883729,SRX5669537,SRS4612406,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,104 2 B03 KOsema3fb tbx18 1,GSM3718964,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,104 2 B03 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718964,GSM3718964: 104 2 B03 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718964,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,104-2-B03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 104-2-B03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,115513857.0,770881.0,GSM3718964 r1,0:74.92 1:74.92,A:31108404;C:26544217;G:27186178;T:30628629;N:46429,74,74,,,31108404,26544217,27186178,30628629,46429,SRX5669537,SRS4612406,SRA798477,GEO,University of Oxford,2,0.88682,0.88375,0.21439,0.21595,0.93787,0.93736,0.51052,0.51032,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49944,SRR8883728,SRX5669536,SRS4612405,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,103 2 B02 KOsema3fb tbx18 1,GSM3718963,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,103 2 B02 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718963,GSM3718963: 103 2 B02 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718963,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,103-2-B02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 103-2-B02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,192832844.0,1295164.0,GSM3718963 r1,0:74.44 1:74.44,A:52098091;C:43785153;G:45595134;T:51197425;N:157041,74,74,,,52098091,43785153,45595134,51197425,157041,SRX5669536,SRS4612405,SRA798477,GEO,University of Oxford,2,0.81383,0.80831,0.24437,0.24477,0.95586,0.95668,0.78895,0.7856,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49945,SRR8883727,SRX5669535,SRS4612404,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,102 2 B01 KOsema3fb tbx18 1,GSM3718962,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,102 2 B01 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718962,GSM3718962: 102 2 B01 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718962,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,102-2-B01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 102-2-B01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,120333848.0,804439.0,GSM3718962 r1,0:74.79 1:74.79,A:32682684;C:27190840;G:28132999;T:32250173;N:77152,74,74,,,32682684,27190840,28132999,32250173,77152,SRX5669535,SRS4612404,SRA798477,GEO,University of Oxford,2,0.83759,0.83074,0.21978,0.21999,0.936,0.93647,0.56733,0.56679,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49946,SRR8883726,SRX5669534,SRS4612403,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,101 2 A12 KOsema3fb tbx18 1,GSM3718961,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,101 2 A12 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718961,GSM3718961: 101 2 A12 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718961,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,101-2-A12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 101-2-A12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,65436843.0,438922.0,GSM3718961 r1,0:74.54 1:74.54,A:17612386;C:14944988;G:15465948;T:17344793;N:68728,74,74,,,17612386,14944988,15465948,17344793,68728,SRX5669534,SRS4612403,SRA798477,GEO,University of Oxford,2,0.85881,0.85199,0.28877,0.28733,0.95826,0.95893,0.76754,0.62031,71,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49947,SRR8883725,SRX5669533,SRS4612402,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,100 2 A11 KOsema3fb tbx18 1,GSM3718960,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,100 2 A11 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718960,GSM3718960: 100 2 A11 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718960,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718960,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,100-2-A11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 100-2-A11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,140310657.0,949434.0,GSM3718960 r1,0:73.89 1:73.89,A:42097554;C:28046328;G:29209965;T:40762460;N:194350,73,73,,,42097554,28046328,29209965,40762460,194350,SRX5669533,SRS4612402,SRA798477,GEO,University of Oxford,2,0.87505,0.86715,0.0038,0.00397,0.99845,0.99866,0.9972,0.97282,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49948,SRR8883724,SRX5669532,SRS4612401,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,099 2 A10 KOsema3fb tbx18 1,GSM3718959,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,099 2 A10 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718959,GSM3718959: 099 2 A10 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718959,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718959,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,099-2-A10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 099-2-A10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,132323171.0,896345.0,GSM3718959 r1,0:73.81 1:73.81,A:35858895;C:29635963;G:31229716;T:35354644;N:243953,73,73,,,35858895,29635963,31229716,35354644,243953,SRX5669532,SRS4612401,SRA798477,GEO,University of Oxford,2,0.77424,0.76268,0.22514,0.2202,0.98652,0.98695,0.86437,0.87792,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49949,SRR8883723,SRX5669531,SRS4612400,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,098 2 A09 KOsema3fb tbx18 1,GSM3718958,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,098 2 A09 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718958,GSM3718958: 098 2 A09 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718958,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718958,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,098-2-A09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 098-2-A09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,114456948.0,771559.0,GSM3718958 r1,0:74.17 1:74.17,A:31737943;C:25279629;G:26036188;T:31288498;N:114690,74,74,,,31737943,25279629,26036188,31288498,114690,SRX5669531,SRS4612400,SRA798477,GEO,University of Oxford,2,0.87167,0.86804,0.23167,0.23179,0.92011,0.92062,0.53072,0.5313,74,74,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49950,SRR8883722,SRX5669530,SRS4612399,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,097 2 A08 KOsema3fb tbx18 1,GSM3718957,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,097 2 A08 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718957,GSM3718957: 097 2 A08 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718957,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718957,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,097-2-A08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 097-2-A08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,73333087.0,494843.0,GSM3718957 r1,0:74.08 1:74.11,A:20100557;C:16284330;G:17212076;T:19600158;N:135966,74,74,,,20100557,16284330,17212076,19600158,135966,SRX5669530,SRS4612399,SRA798477,GEO,University of Oxford,2,0.58813,0.57236,0.34093,0.32937,0.98839,0.98851,0.779,0.72827,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49951,SRR8883721,SRX5669529,SRS4612398,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,096 2 A06 KOsema3fb tbx18 1,GSM3718956,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,096 2 A06 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718956,GSM3718956: 096 2 A06 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718956,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718956,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,096-2-A06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 096-2-A06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,90842172.0,611862.0,GSM3718956 r1,0:74.23 1:74.24,A:23965966;C:21373491;G:21862424;T:23547639;N:92652,74,74,,,23965966,21373491,21862424,23547639,92652,SRX5669529,SRS4612398,SRA798477,GEO,University of Oxford,2,0.8843,0.88141,0.07106,0.07335,0.95152,0.95134,0.66617,0.66026,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49952,SRR8883720,SRX5669528,SRS4612397,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,095 2 A05 KOsema3fb tbx18 1,GSM3718955,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,095 2 A05 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718955,GSM3718955: 095 2 A05 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718955,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,095-2-A05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 095-2-A05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,77815127.0,524581.0,GSM3718955 r1,0:74.18 1:74.16,A:21934006;C:16958511;G:17457568;T:21408772;N:56270,74,74,,,21934006,16958511,17457568,21408772,56270,SRX5669528,SRS4612397,SRA798477,GEO,University of Oxford,2,0.91045,0.90324,0.15048,0.14704,0.90611,0.90778,0.61827,0.61537,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49953,SRR8883719,SRX5669527,SRS4612396,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,094 2 A04 KOsema3fb tbx18 1,GSM3718954,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,094 2 A04 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718954,GSM3718954: 094 2 A04 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718954,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718954,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,094-2-A04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 094-2-A04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,150930160.0,1017672.0,GSM3718954 r1,0:74.15 1:74.16,A:46095353;C:29229977;G:30487780;T:44969159;N:147891,74,74,,,46095353,29229977,30487780,44969159,147891,SRX5669527,SRS4612396,SRA798477,GEO,University of Oxford,2,0.89968,0.89516,0.15644,0.15583,0.98965,0.98957,0.90884,0.88342,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49954,SRR8883718,SRX5669526,SRS4612395,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,093 2 A03 KOsema3fb tbx18 1,GSM3718953,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,093 2 A03 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718953,GSM3718953: 093 2 A03 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718953,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718953,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,093-2-A03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 093-2-A03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,144217761.0,973753.0,GSM3718953 r1,0:74.05 1:74.06,A:39154057;C:32680762;G:33686996;T:38528147;N:167799,74,74,,,39154057,32680762,33686996,38528147,167799,SRX5669526,SRS4612395,SRA798477,GEO,University of Oxford,2,0.85323,0.8494,0.3006,0.30141,0.94655,0.94679,0.58374,0.59101,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49955,SRR8883717,SRX5669525,SRS4612394,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,092 2 A02 KOsema3fb tbx18 1,GSM3718952,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,092 2 A02 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718952,GSM3718952: 092 2 A02 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718952,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,092-2-A02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 092-2-A02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,124615116.0,836655.0,GSM3718952 r1,0:74.47 1:74.47,A:29165184;C:32964210;G:34113962;T:28256712;N:115048,74,74,,,29165184,32964210,34113962,28256712,115048,SRX5669525,SRS4612394,SRA798477,GEO,University of Oxford,2,0.80508,0.80178,0.26378,0.26378,0.99141,0.99133,0.707,0.65919,73,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49956,SRR8883716,SRX5669524,SRS4612393,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,091 2 A01 KOsema3fb tbx18 1,GSM3718951,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,091 2 A01 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718951,GSM3718951: 091 2 A01 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718951,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718951,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,091-2-A01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 091-2-A01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,130111864.0,870690.0,GSM3718951 r1,0:74.72 1:74.72,A:37160441;C:27653019;G:28922504;T:36294701;N:81199,74,74,,,37160441,27653019,28922504,36294701,81199,SRX5669524,SRS4612393,SRA798477,GEO,University of Oxford,2,0.8646,0.85823,0.13494,0.13789,0.9934,0.9933,0.94953,0.94841,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49957,SRR8883715,SRX5669523,SRS4612392,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,090 1 H12 KOsema3fb tbx18 1,GSM3718950,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,090 1 H12 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718950,GSM3718950: 090 1 H12 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718950,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718950,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,090-1-H12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 090-1-H12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,149578485.0,1002183.0,GSM3718950 r1,0:74.63 1:74.62,A:38597080;C:36561279;G:37234713;T:37123758;N:61655,74,74,,,38597080,36561279,37234713,37123758,61655,SRX5669523,SRS4612392,SRA798477,GEO,University of Oxford,2,0.91419,0.91521,0.10566,0.10682,0.93143,0.93133,0.63762,0.63312,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49958,SRR8883714,SRX5669522,SRS4612391,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,089 1 H11 KOsema3fb tbx18 1,GSM3718949,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,089 1 H11 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718949,GSM3718949: 089 1 H11 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718949,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718949,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,089-1-H11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 089-1-H11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz,fastq fastq,181404476.0,1216282.0,GSM3718949 r1,0:74.57 1:74.57,A:43064417;C:47397029;G:49107412;T:41710650;N:124968,74,74,,,43064417,47397029,49107412,41710650,124968,SRX5669522,SRS4612391,SRA798477,GEO,University of Oxford,2,0.77119,0.76546,0.25328,0.25162,0.99371,0.99375,0.7712,0.79784,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49959,SRR8883713,SRX5669521,SRS4612390,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,088 1 H10 KOsema3fb tbx18 1,GSM3718948,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,088 1 H10 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718948,GSM3718948: 088 1 H10 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718948,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718948,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,088-1-H10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 088-1-H10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,141673238.0,952834.0,GSM3718948 r1,0:74.34 1:74.34,A:34350000;C:36603083;G:37520883;T:33109631;N:89641,74,74,,,34350000,36603083,37520883,33109631,89641,SRX5669521,SRS4612390,SRA798477,GEO,University of Oxford,2,0.79667,0.79244,0.28634,0.28347,0.96366,0.96321,0.6333,0.68112,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49960,SRR8883712,SRX5669520,SRS4612389,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,087 1 H09 KOsema3fb tbx18 1,GSM3718947,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,087 1 H09 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718947,GSM3718947: 087 1 H09 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718947,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718947,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,087-1-H09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 087-1-H09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,156833870.0,1059269.0,GSM3718947 r1,0:74.04 1:74.02,A:39115526;C:39464692;G:40259183;T:37861574;N:132895,74,74,,,39115526,39464692,40259183,37861574,132895,SRX5669520,SRS4612389,SRA798477,GEO,University of Oxford,2,0.83542,0.83393,0.10395,0.10686,0.97532,0.9753,0.6127,0.61353,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49961,SRR8883711,SRX5669519,SRS4612388,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,086 1 H08 KOsema3fb tbx18 1,GSM3718946,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,086 1 H08 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718946,GSM3718946: 086 1 H08 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718946,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718946,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,086-1-H08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 086-1-H08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,141486517.0,946739.0,GSM3718946 r1,0:74.73 1:74.72,A:34720035;C:36172265;G:36926372;T:33608900;N:58945,74,74,,,34720035,36172265,36926372,33608900,58945,SRX5669519,SRS4612388,SRA798477,GEO,University of Oxford,2,0.85483,0.854,0.13126,0.13493,0.96917,0.96938,0.56895,0.57342,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System
49962,SRR8883710,SRX5669518,SRS4612387,SRP166782,PRJNA498309,Functional heterogeneity within the developing zebrafish epicardium,GSE121750,Transcriptome Analysis,The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells,,pubmed:32084358,,085 1 H07 KOsema3fb tbx18 1,GSM3718945,,tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,085 1 H07 KOsema3fb tbx18 1,Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC,Heart,,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,,transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf,GSM3718945,GSM3718945: 085 1 H07 KOsema3fb tbx18 1; Danio rerio; RNA Seq,GSM3718945,,1,Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT,GEO Accession:GSM3718945,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP166782,,,085-1-H07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 085-1-H07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz,fastq fastq,160038205.0,1074199.0,GSM3718945 r1,0:74.49 1:74.49,A:42350221;C:37069067;G:38413049;T:42051865;N:154003,74,74,,,42350221,37069067,38413049,42051865,154003,SRX5669518,SRS4612387,SRA798477,GEO,University of Oxford,2,0.73986,0.73837,0.33609,0.33447,0.97619,0.97615,0.73697,0.72259,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-11,Larval,Larval,Heart,Cardiovascular System