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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", null, null, null, null, null, null, null, null, "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 40\u03bcm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. 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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", null, null, null, null, null, null, null, null, "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 40\u03bcm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. 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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", null, null, "E MTAB 4617:LCK 7#90", "0:125 1:125", "A:106342222;C:98049090;G:91971650;T:111243138;N:46400", 125, 125, null, null, 106342222, 98049090, 91971650, 111243138, 46400, "ERX1497955", null, "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", null, "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. 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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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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. 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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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#89", "0:125 1:125", "A:53847121;C:51852010;G:47816940;T:57047962;N:23717", 125, 125, null, null, 53847121, 51852010, 47816940, 57047962, 23717, "ERX1497953", null, "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", null, "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. 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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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#83", "0:125 1:125", "A:73686338;C:69380167;G:63301440;T:77949626;N:35429", 125, 125, null, null, 73686338, 69380167, 63301440, 77949626, 35429, "ERX1497947", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#82", "0:125 1:125", "A:132306808;C:126337107;G:118115874;T:139760194;N:65267", 125, 125, null, null, 132306808, 126337107, 118115874, 139760194, 65267, "ERX1497946", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#81", "0:125 1:125", "A:49752056;C:47569625;G:43787172;T:52848426;N:21471", 125, 125, null, null, 49752056, 47569625, 43787172, 52848426, 21471, "ERX1497945", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#75", "0:125 1:125", "A:215270392;C:173814423;G:161953517;T:222035470;N:96448", 125, 125, null, null, 215270392, 173814423, 161953517, 222035470, 96448, "ERX1497938", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#74", "0:125 1:125", "A:123931531;C:111767107;G:106439636;T:128665381;N:58095", 125, 125, null, null, 123931531, 111767107, 106439636, 128665381, 58095, "ERX1497937", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#73", "0:125 1:125", "A:47487658;C:44369011;G:41797745;T:49759850;N:22236", 125, 125, null, null, 47487658, 44369011, 41797745, 49759850, 22236, "ERX1497936", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#67", "0:125 1:125", "A:211181074;C:167361986;G:152479010;T:214248000;N:87930", 125, 125, null, null, 211181074, 167361986, 152479010, 214248000, 87930, "ERX1497929", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#66", "0:125 1:125", "A:122494933;C:109921862;G:103257549;T:125665684;N:56722", 125, 125, null, null, 122494933, 109921862, 103257549, 125665684, 56722, "ERX1497928", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#65", "0:125 1:125", "A:96259909;C:89965165;G:84222055;T:99868995;N:43376", 125, 125, null, null, 96259909, 89965165, 84222055, 99868995, 43376, "ERX1497927", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#59", "0:125 1:125", "A:134247255;C:121203898;G:112067297;T:140566781;N:62269", 125, 125, null, null, 134247255, 121203898, 112067297, 140566781, 62269, "ERX1497920", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#58", "0:125 1:125", "A:165043952;C:161634321;G:152303735;T:174314970;N:75022", 125, 125, null, null, 165043952, 161634321, 152303735, 174314970, 75022, "ERX1497919", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#57", "0:125 1:125", "A:81845074;C:82172065;G:76757417;T:87625766;N:38678", 125, 125, null, null, 81845074, 82172065, 76757417, 87625766, 38678, "ERX1497918", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#51", "0:125 1:125", "A:68083321;C:57560520;G:49834107;T:71348826;N:28226", 125, 125, null, null, 68083321, 57560520, 49834107, 71348826, 28226, "ERX1497912", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#50", "0:125 1:125", "A:200436684;C:191639110;G:173623845;T:213497904;N:94207", 125, 125, null, null, 200436684, 191639110, 173623845, 213497904, 94207, "ERX1497911", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#49", "0:125 1:125", "A:96840239;C:94376256;G:85197984;T:104185788;N:45483", 125, 125, null, null, 96840239, 94376256, 85197984, 104185788, 45483, "ERX1497909", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#43", "0:125 1:125", "A:95132366;C:87995738;G:81475905;T:100137372;N:45119", 125, 125, null, null, 95132366, 87995738, 81475905, 100137372, 45119, "ERX1497903", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#42", "0:125 1:125", "A:45015627;C:40505684;G:37787157;T:46787414;N:20618", 125, 125, null, null, 45015627, 40505684, 37787157, 46787414, 20618, "ERX1497902", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#41", "0:125 1:125", "A:89502636;C:89074499;G:83078909;T:95568395;N:39311", 125, 125, null, null, 89502636, 89074499, 83078909, 95568395, 39311, "ERX1497901", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#35", "0:125 1:125", "A:139844227;C:137312069;G:126169914;T:149207606;N:69934", 125, 125, null, null, 139844227, 137312069, 126169914, 149207606, 69934, "ERX1497894", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#34", "0:125 1:125", "A:134481938;C:127574886;G:118538403;T:142102568;N:61455", 125, 125, null, null, 134481938, 127574886, 118538403, 142102568, 61455, "ERX1497893", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#33", "0:125 1:125", "A:93220735;C:94390552;G:86770054;T:100705096;N:43313", 125, 125, null, null, 93220735, 94390552, 86770054, 100705096, 43313, "ERX1497892", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#3", "0:125 1:125", "A:58493174;C:54183075;G:50060440;T:61036959;N:28352", 125, 125, null, null, 58493174, 54183075, 50060440, 61036959, 28352, "ERX1497888", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#27", "0:125 1:125", "A:116175271;C:110956295;G:101584573;T:123371066;N:51045", 125, 125, null, null, 116175271, 110956295, 101584573, 123371066, 51045, "ERX1497885", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#26", "0:125 1:125", "A:84022783;C:79751329;G:73366671;T:88820379;N:40588", 125, 125, null, null, 84022783, 79751329, 73366671, 88820379, 40588, "ERX1497884", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#25", "0:125 1:125", "A:93291373;C:90572911;G:83617400;T:99965116;N:42450", 125, 125, null, null, 93291373, 90572911, 83617400, 99965116, 42450, "ERX1497883", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#2", "0:125 1:125", "A:50810642;C:45505266;G:42437381;T:52252338;N:22373", 125, 125, null, null, 50810642, 45505266, 42437381, 52252338, 22373, "ERX1497877", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#19", "0:125 1:125", "A:123448577;C:117648440;G:109679332;T:127799152;N:59249", 125, 125, null, null, 123448577, 117648440, 109679332, 127799152, 59249, "ERX1497876", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#18", "0:125 1:125", "A:116722795;C:108761302;G:102297772;T:120311653;N:53978", 125, 125, null, null, 116722795, 108761302, 102297772, 120311653, 53978, "ERX1497875", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#17", "0:125 1:125", "A:114273839;C:106761242;G:100217178;T:118680369;N:52122", 125, 125, null, null, 114273839, 106761242, 100217178, 118680369, 52122, "ERX1497874", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#11", "0:125 1:125", "A:94603298;C:90252097;G:83046109;T:99899414;N:44332", 125, 125, null, null, 94603298, 90252097, 83046109, 99899414, 44332, "ERX1497868", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#10", "0:125 1:125", "A:136048498;C:130651014;G:121379521;T:142822578;N:64889", 125, 125, null, null, 136048498, 130651014, 121379521, 142822578, 64889, "ERX1497867", null, "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", null, "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", null, "Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40\u03bcm 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", null, null, null, null, null, null, null, null, "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 40\u03bcm 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", null, null, "E MTAB 4617:LCK 7#1", "0:125 1:125", "A:128250593;C:122748202;G:114418508;T:135400263;N:59934", 125, 125, null, null, 128250593, 122748202, 114418508, 135400263, 59934, "ERX1497866", null, "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", null, "Switzerland", "2016-05-26", "Adult", "Adult", "Heart", "Cardiovascular System"], [25320, "SRR25810878", "SRX21533024", "SRS18745490", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 wild type siblings 2", "GSM7745909", null, "source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing", "egr3 wild type siblings 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577+/+", "GSM7745909", "GSM7745909: egr3 wild type siblings 2; Danio rerio; RNA Seq", "GSM7745909 r1", "GSM7745909", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_WT2_R1.fastq.gz", "fastq", 3473319384.0, 49279465.0, "GSM7745909 r1", "0:70.48", "A:943794847;C:792135324;G:792042625;T:945083925;N:262663", 70, null, null, null, 943794847, 792135324, 792042625, 945083925, 262663, "SRX21533024", "SRS18745490", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.68549, null, 0.04588, null, 0.76865, null, 0.44964, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [25321, "SRR25810879", "SRX21533023", "SRS18745489", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 wild type siblings 1", "GSM7745908", null, "source name:Heart|tissue:Heart|genotype:bns577+/+|geo loc name:missing|collection date:missing", "egr3 wild type siblings 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577+/+", "GSM7745908", "GSM7745908: egr3 wild type siblings 1; Danio rerio; RNA Seq", "GSM7745908 r1", "GSM7745908", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_WT1_R1.fastq.gz", "fastq", 3909248616.0, 55045571.0, "GSM7745908 r1", "0:71.02", "A:1048107387;C:905014546;G:907455489;T:1048528690;N:142504", 71, null, null, null, 1048107387, 905014546, 907455489, 1048528690, 142504, "SRX21533023", "SRS18745489", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94958, null, 0.06298, null, 0.74819, null, 0.45762, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [25322, "SRR25810880", "SRX21533022", "SRS18745488", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 mutants 2", "GSM7745907", null, "source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing", "egr3 mutants 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577 / ", "GSM7745907", "GSM7745907: egr3 mutants 2; Danio rerio; RNA Seq", "GSM7745907 r1", "GSM7745907", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_Mut2_R1.fastq.gz", "fastq", 3432675258.0, 48483287.0, "GSM7745907 r1", "0:70.80", "A:925832958;C:788551205;G:790129536;T:927993012;N:168547", 70, null, null, null, 925832958, 788551205, 790129536, 927993012, 168547, "SRX21533022", "SRS18745488", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.75652, null, 0.04046, null, 0.76455, null, 0.46333, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [25323, "SRR25810881", "SRX21533021", "SRS18745487", "SRP457576", "PRJNA1010780", "Effect of egr3 knockout on gene expression of dissected zebrafish hearts", "GSE241935", "Transcriptome Analysis", "To screen for Egr3 targets mediating cardiac valve development we assessed gene expression on dissected hearts of egr3 mutants and wild type siblings. Overall design: To evaluate the transcriptional differences underlying the egr3 mutant phenotype  we conducted a bulk RNA seq analysis in dissected zebrafish hearts at 48 hpf.  We dissected 20 hearts for each biological duplicate of egr3 mutant and wild type sibling samples in cold DMEM with 10% FBS.  Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u00b5l of RNase free water.   Analysis of the obtained reads confirmed the 11bp deletion in the mutant samples.   1. Boezio  G. L. M. et al. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 16 2023. https://doi.org:10.1242/dmm.049571", null, "pubmed:38748804", null, "egr3 mutants 1", "GSM7745906", null, "source name:Heart|tissue:Heart|genotype:bns577 / |geo loc name:missing|collection date:missing", "egr3 mutants 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 2.27.1 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.30.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2 and batch corrected using CountClust each biological replicate = one batch Dey K et al.  Visualizing the structure of RNA seq expression data using grade of membership models. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. Assembly: danRer11 Supplementary files format and content: libryr size notmalize amd batch corrected counts", "Heart", null, "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "tissue:Heart|genotype:bns577 / ", "GSM7745906", "GSM7745906: egr3 mutants 1; Danio rerio; RNA Seq", "GSM7745906 r1", "GSM7745906", "1", "Total RNA was isolated using the miRNeasy micro Kit Qiagen 217084  followed by on column DNase digestion DNase Free DNase Set  Qiagen 79254  and final elution was performed in 12\u03bcl of RNase free water 10ng total RNA was used for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP457576", null, "loader:fastq load.py", "E22_3626_Lib_Agatha_egr3_Mut1_R1.fastq.gz", "fastq", 3838969347.0, 54545950.0, "GSM7745906 r1", "0:70.38", "A:1016913415;C:902500250;G:903033204;T:1016194618;N:327860", 70, null, null, null, 1016913415, 902500250, 903033204, 1016194618, 327860, "SRX21533021", "SRS18745487", "SRA1702458", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9511, null, 0.05017, null, 0.75341, null, 0.47152, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-08-30", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [49040, "SRR7633494", "SRX4497225", "SRS3618225", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G2 endo 03", "GSM3317066", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA", "G2 endo 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G2 mRNA", "GSM3317066", "GSM3317066: G2 endo 03; Danio rerio; RNA Seq", "GSM3317066", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S18_trimmed.fastq.gz", "fastq", 950344310.0, 18847513.0, "GSM3317066 r1", "0:50.42 1:0", "A:270135652;C:209210468;G:202674675;T:268256430;N:67085", 50, 0, null, null, 270135652, 209210468, 202674675, 268256430, 67085, "SRX4497225", "SRS3618225", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89759, null, 0.1428, null, 0.69132, null, 0.4729, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49041, "SRR7633493", "SRX4497224", "SRS3618224", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G2 endo 02", "GSM3317065", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA", "G2 endo 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G2 mRNA", "GSM3317065", "GSM3317065: G2 endo 02; Danio rerio; RNA Seq", "GSM3317065", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S17_trimmed.fastq.gz", "fastq", 1635110054.0, 32380584.0, "GSM3317065 r1", "0:50.50 1:0", "A:462134552;C:361057634;G:349465446;T:462337205;N:115217", 50, 0, null, null, 462134552, 361057634, 349465446, 462337205, 115217, "SRX4497224", "SRS3618224", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.80201, null, 0.12711, null, 0.70471, null, 0.44427, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49042, "SRR7633492", "SRX4497223", "SRS3618223", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G2 endo 01", "GSM3317064", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA", "G2 endo 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G2 mRNA", "GSM3317064", "GSM3317064: G2 endo 01; Danio rerio; RNA Seq", "GSM3317064", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S16_trimmed.fastq.gz", "fastq", 1302352614.0, 25794210.0, "GSM3317064 r1", "0:50.49 1:0", "A:370194702;C:286011167;G:276758200;T:369297736;N:90809", 50, 0, null, null, 370194702, 286011167, 276758200, 369297736, 90809, "SRX4497223", "SRS3618223", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89468, null, 0.15745, null, 0.69447, null, 0.47938, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49043, "SRR7633491", "SRX4497222", "SRS3618222", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G0 endo 03", "GSM3317063", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA", "G0 endo 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G0 mRNA", "GSM3317063", "GSM3317063: G0 endo 03; Danio rerio; RNA Seq", "GSM3317063", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317063", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S15_trimmed.fastq.gz", "fastq", 1248556473.0, 24725241.0, "GSM3317063 r1", "0:50.50 1:0", "A:350256976;C:280431139;G:270771772;T:347009294;N:87292", 50, 0, null, null, 350256976, 280431139, 270771772, 347009294, 87292, "SRX4497222", "SRS3618222", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.90514, null, 0.13266, null, 0.69236, null, 0.47977, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49044, "SRR7633490", "SRX4497221", "SRS3618221", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G0 endo 02", "GSM3317062", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA", "G0 endo 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G0 mRNA", "GSM3317062", "GSM3317062: G0 endo 02; Danio rerio; RNA Seq", "GSM3317062", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317062", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S14_trimmed.fastq.gz", "fastq", 372093672.0, 7456111.0, "GSM3317062 r1", "0:49.90 1:0", "A:113486766;C:74400549;G:71245468;T:112935661;N:25228", 49, 0, null, null, 113486766, 74400549, 71245468, 112935661, 25228, "SRX4497221", "SRS3618221", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.89644, null, 0.12968, null, 0.70658, null, 0.47231, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49045, "SRR7633489", "SRX4497220", "SRS3618220", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "G0 endo 01", "GSM3317061", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA", "G0 endo 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:human APOL1 G0 mRNA", "GSM3317061", "GSM3317061: G0 endo 01; Danio rerio; RNA Seq", "GSM3317061", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S13_trimmed.fastq.gz", "fastq", 1450133780.0, 28705598.0, "GSM3317061 r1", "0:50.52 1:0", "A:407543677;C:323333189;G:313321100;T:405835253;N:100561", 50, 0, null, null, 407543677, 323333189, 313321100, 405835253, 100561, "SRX4497220", "SRS3618220", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.8994, null, 0.13347, null, 0.6942, null, 0.47759, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49046, "SRR7633488", "SRX4497219", "SRS3618219", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "control endo 03", "GSM3317060", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:control", "control endo 03", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:control", "GSM3317060", "GSM3317060: control endo 03; Danio rerio; RNA Seq", "GSM3317060", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S12_trimmed.fastq.gz", "fastq", 1720199608.0, 34019943.0, "GSM3317060 r1", "0:50.56 1:0", "A:474252335;C:393152371;G:382256277;T:470417173;N:121452", 50, 0, null, null, 474252335, 393152371, 382256277, 470417173, 121452, "SRX4497219", "SRS3618219", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.90252, null, 0.11709, null, 0.69668, null, 0.47424, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49047, "SRR7633487", "SRX4497218", "SRS3618218", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "control endo 02", "GSM3317059", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:control", "control endo 02", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:control", "GSM3317059", "GSM3317059: control endo 02; Danio rerio; RNA Seq", "GSM3317059", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317059", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S11_trimmed.fastq.gz", "fastq", 322327295.0, 6605687.0, "GSM3317059 r1", "0:48.80 1:0", "A:109722776;C:53179948;G:51091267;T:108312123;N:21181", 48, 0, null, null, 109722776, 53179948, 51091267, 108312123, 21181, "SRX4497218", "SRS3618218", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.8922, null, 0.1261, null, 0.72811, null, 0.46128, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49048, "SRR7633486", "SRX4497217", "SRS3618217", "SRP155992", "PRJNA483985", "Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA", "GSE118000", "Transcriptome Analysis", "We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2", null, "pubmed:31158233", null, "control endo 01", "GSM3317058", null, "tissue:zebrafish endothelium|line:fli:EGFP|treatment:control", "control endo 01", "Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2", "zebrafish endothelium", "Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf", "line:fli:EGFP|treatment:control", "GSM3317058", "GSM3317058: control endo 01; Danio rerio; RNA Seq", "GSM3317058", null, "1", "RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech", "GEO Accession:GSM3317058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155992", null, null, "BA_S10_trimmed.fastq.gz", "fastq", 1484074935.0, 29385409.0, "GSM3317058 r1", "0:50.50 1:0", "A:411414710;C:336260838;G:326730208;T:409563857;N:105322", 50, 0, null, null, 411414710, 336260838, 326730208, 409563857, 105322, "SRX4497217", "SRS3618217", "SRA749599", "GEO", "Duke Molecular Physiology Institute, Duke University Medical Center", 1, 0.88777, null, 0.11462, null, 0.70102, null, 0.47353, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2018-08-01", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [49850, "SRR8883829", "SRX5669659", "SRS4612528", "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", null, "pubmed:32084358", null, "148 2 E12 KOcxcl12a 6 reseq", "GSM3719057", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "148 2 E12 KOcxcl12a 6 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719057", "GSM3719057: 148 2 E12 KOcxcl12a 6 reseq; Danio rerio; RNA Seq", "GSM3719057", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "148-2-E12-KOcxcl12a-6_reseq_all_lanes_R1.fastq.gz", "fastq", 763065205.0, 10372479.0, "GSM3719057 r1", "0:73.57 1:0", "A:179985921;C:199425581;G:205920814;T:177110327;N:622562", 73, 0, null, null, 179985921, 199425581, 205920814, 177110327, 622562, "SRX5669659", "SRS4612528", "SRA798477", "GEO", "University of Oxford", 1, 0.93161, null, 0.2297, null, 0.75684, null, 0.64613, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49851, "SRR8883828", "SRX5669658", "SRS4612527", "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", null, "pubmed:32084358", null, "147 2 E11 KOcxcl12a 5 reseq", "GSM3719056", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "147 2 E11 KOcxcl12a 5 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719056", "GSM3719056: 147 2 E11 KOcxcl12a 5 reseq; Danio rerio; RNA Seq", "GSM3719056", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "147-2-E11-KOcxcl12a-5_reseq_all_lanes_R1.fastq.gz", "fastq", 777154556.0, 10544824.0, "GSM3719056 r1", "0:73.70 1:0", "A:182318789;C:204282719;G:210781481;T:179272833;N:498734", 73, 0, null, null, 182318789, 204282719, 210781481, 179272833, 498734, "SRX5669658", "SRS4612527", "SRA798477", "GEO", "University of Oxford", 1, 0.94256, null, 0.25229, null, 0.76781, null, 0.67336, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49852, "SRR8883827", "SRX5669657", "SRS4612526", "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", null, "pubmed:32084358", null, "146 2 E10 KOcxcl12a 4 reseq", "GSM3719055", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "146 2 E10 KOcxcl12a 4 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719055", "GSM3719055: 146 2 E10 KOcxcl12a 4 reseq; Danio rerio; RNA Seq", "GSM3719055", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719055", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "146-2-E10-KOcxcl12a-4_reseq_all_lanes_R1.fastq.gz", "fastq", 893756036.0, 12231836.0, "GSM3719055 r1", "0:73.07 1:0", "A:208987215;C:235365706;G:243090724;T:205234077;N:1078314", 73, 0, null, null, 208987215, 235365706, 243090724, 205234077, 1078314, "SRX5669657", "SRS4612526", "SRA798477", "GEO", "University of Oxford", 1, 0.93675, null, 0.21776, null, 0.76597, null, 0.63391, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49853, "SRR8883826", "SRX5669656", "SRS4612525", "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", null, "pubmed:32084358", null, "145 2 E09 KOcxcl12a 3 reseq", "GSM3719054", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "145 2 E09 KOcxcl12a 3 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719054", "GSM3719054: 145 2 E09 KOcxcl12a 3 reseq; Danio rerio; RNA Seq", "GSM3719054", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "145-2-E09-KOcxcl12a-3_reseq_all_lanes_R1.fastq.gz", "fastq", 850857048.0, 11668488.0, "GSM3719054 r1", "0:72.92 1:0", "A:205769666;C:217594988;G:223805195;T:202463052;N:1224147", 72, 0, null, null, 205769666, 217594988, 223805195, 202463052, 1224147, "SRX5669656", "SRS4612525", "SRA798477", "GEO", "University of Oxford", 1, 0.92738, null, 0.2566, null, 0.75152, null, 0.65144, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49854, "SRR8883825", "SRX5669655", "SRS4612524", "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", null, "pubmed:32084358", null, "144 2 E08 KOcxcl12a 2 reseq", "GSM3719053", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "144 2 E08 KOcxcl12a 2 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719053", "GSM3719053: 144 2 E08 KOcxcl12a 2 reseq; Danio rerio; RNA Seq", "GSM3719053", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "144-2-E08-KOcxcl12a-2_reseq_all_lanes_R1.fastq.gz", "fastq", 898577334.0, 12271421.0, "GSM3719053 r1", "0:73.23 1:0", "A:209765901;C:237376777;G:244548553;T:205953258;N:932845", 73, 0, null, null, 209765901, 237376777, 244548553, 205953258, 932845, "SRX5669655", "SRS4612524", "SRA798477", "GEO", "University of Oxford", 1, 0.94312, null, 0.22115, null, 0.75751, null, 0.63782, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49855, "SRR8883824", "SRX5669654", "SRS4612523", "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", null, "pubmed:32084358", null, "143 2 E07 KOcxcl12a 1 reseq", "GSM3719052", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "143 2 E07 KOcxcl12a 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719052", "GSM3719052: 143 2 E07 KOcxcl12a 1 reseq; Danio rerio; RNA Seq", "GSM3719052", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "143-2-E07-KOcxcl12a-1_reseq_all_lanes_R1.fastq.gz", "fastq", 642191206.0, 8724687.0, "GSM3719052 r1", "0:73.61 1:0", "A:148702964;C:170638392;G:176459501;T:145895525;N:494824", 73, 0, null, null, 148702964, 170638392, 176459501, 145895525, 494824, "SRX5669654", "SRS4612523", "SRA798477", "GEO", "University of Oxford", 1, 0.93805, null, 0.20319, null, 0.76203, null, 0.65533, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49856, "SRR8883823", "SRX5669653", "SRS4612522", "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", null, "pubmed:32084358", null, "142 2 E06 KOcxcl12a ctr 3 reseq", "GSM3719051", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "142 2 E06 KOcxcl12a ctr 3 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719051", "GSM3719051: 142 2 E06 KOcxcl12a ctr 3 reseq; Danio rerio; RNA Seq", "GSM3719051", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "142-2-E06-KOcxcl12a-ctr-3_reseq_all_lanes_R1.fastq.gz", "fastq", 913646709.0, 12532356.0, "GSM3719051 r1", "0:72.90 1:0", "A:210664396;C:243042644;G:251444631;T:207071337;N:1423701", 72, 0, null, null, 210664396, 243042644, 251444631, 207071337, 1423701, "SRX5669653", "SRS4612522", "SRA798477", "GEO", "University of Oxford", 1, 0.93582, null, 0.21132, null, 0.7669, null, 0.65882, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49857, "SRR8883822", "SRX5669652", "SRS4612521", "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", null, "pubmed:32084358", null, "141 2 E05 KOcxcl12a ctr 2 reseq", "GSM3719050", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "141 2 E05 KOcxcl12a ctr 2 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719050", "GSM3719050: 141 2 E05 KOcxcl12a ctr 2 reseq; Danio rerio; RNA Seq", "GSM3719050", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "141-2-E05-KOcxcl12a-ctr-2_reseq_all_lanes_R1.fastq.gz", "fastq", 698256933.0, 9557079.0, "GSM3719050 r1", "0:73.06 1:0", "A:165636445;C:181576831;G:187431558;T:162693862;N:918237", 73, 0, null, null, 165636445, 181576831, 187431558, 162693862, 918237, "SRX5669652", "SRS4612521", "SRA798477", "GEO", "University of Oxford", 1, 0.92623, null, 0.20301, null, 0.75562, null, 0.58643, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49858, "SRR8883821", "SRX5669651", "SRS4612520", "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", null, "pubmed:32084358", null, "140 2 E04 KOcxcl12a ctr 1 reseq", "GSM3719049", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "140 2 E04 KOcxcl12a ctr 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719049", "GSM3719049: 140 2 E04 KOcxcl12a ctr 1 reseq; Danio rerio; RNA Seq", "GSM3719049", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "140-2-E04-KOcxcl12a-ctr-1_reseq_all_lanes_R1.fastq.gz", "fastq", 824049635.0, 11240750.0, "GSM3719049 r1", "0:73.31 1:0", "A:195127513;C:214512790;G:222034432;T:191506323;N:868577", 73, 0, null, null, 195127513, 214512790, 222034432, 191506323, 868577, "SRX5669651", "SRS4612520", "SRA798477", "GEO", "University of Oxford", 1, 0.93289, null, 0.20393, null, 0.75749, null, 0.60814, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49859, "SRR8883820", "SRX5669650", "SRS4612519", "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", null, "pubmed:32084358", null, "130 2 D06 KOsema3fb tbx18 1 reseq", "GSM3719048", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "130 2 D06 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719048", "GSM3719048: 130 2 D06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719048", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "130-2-D06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1162709924.0, 15925191.0, "GSM3719048 r1", "0:73.01 1:0", "A:289120225;C:287784856;G:301546291;T:282206243;N:2052309", 73, 0, null, null, 289120225, 287784856, 301546291, 282206243, 2052309, "SRX5669650", "SRS4612519", "SRA798477", "GEO", "University of Oxford", 1, 0.7653, null, 0.25001, null, 0.98997, null, 0.83422, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49860, "SRR8883819", "SRX5669649", "SRS4612518", "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", null, "pubmed:32084358", null, "124 2 C12 KOsema3fb tbx18 1 reseq", "GSM3719047", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "124 2 C12 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "124-2-C12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 299825780.0, 4022960.0, "GSM3719047 r1", "0:74.53 1:0", "A:68392314;C:78125239;G:84196045;T:69093198;N:18984", 74, 0, null, null, 68392314, 78125239, 84196045, 69093198, 18984, "SRX5669649", "SRS4612518", "SRA798477", "GEO", "University of Oxford", 1, 0.74846, null, 0.27048, null, 0.99557, null, 0.70087, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49861, "SRR8883818", "SRX5669648", "SRS4612517", "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", null, "pubmed:32084358", null, "123 2 C11 KOsema3fb tbx18 1 reseq", "GSM3719046", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "123 2 C11 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719046", "GSM3719046: 123 2 C11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719046", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719046", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "123-2-C11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 295959651.0, 3971786.0, "GSM3719046 r1", "0:74.52 1:0", "A:77279704;C:70402673;G:74373147;T:73882710;N:21417", 74, 0, null, null, 77279704, 70402673, 74373147, 73882710, 21417, "SRX5669648", "SRS4612517", "SRA798477", "GEO", "University of Oxford", 1, 0.82981, null, 0.14333, null, 0.99758, null, 0.91205, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49862, "SRR8883817", "SRX5669647", "SRS4612516", "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", null, "pubmed:32084358", null, "119 2 C07 KOsema3fb tbx18 1 reseq", "GSM3719045", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "119 2 C07 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719045", "GSM3719045: 119 2 C07 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719045", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719045", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "119-2-C07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 264496882.0, 3548156.0, "GSM3719045 r1", "0:74.54 1:0", "A:75579264;C:55698110;G:58441353;T:74755905;N:22250", 74, 0, null, null, 75579264, 55698110, 58441353, 74755905, 22250, "SRX5669647", "SRS4612516", "SRA798477", "GEO", "University of Oxford", 1, 0.80888, null, 0.37987, null, 0.98039, null, 0.91771, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49863, "SRR8883816", "SRX5669646", "SRS4612515", "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", null, "pubmed:32084358", null, "113 2 C01 KOsema3fb tbx18 1 reseq", "GSM3719044", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "113 2 C01 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719044", "GSM3719044: 113 2 C01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719044", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "113-2-C01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 900078149.0, 12264833.0, "GSM3719044 r1", "0:73.39 1:0", "A:219770321;C:225774705;G:235824823;T:217584908;N:1123392", 73, 0, null, null, 219770321, 225774705, 235824823, 217584908, 1123392, "SRX5669646", "SRS4612515", "SRA798477", "GEO", "University of Oxford", 1, 0.7672, null, 0.32569, null, 0.9811, null, 0.69383, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49864, "SRR8883815", "SRX5669645", "SRS4612514", "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", null, "pubmed:32084358", null, "109 2 B08 KOsema3fb tbx18 1 reseq", "GSM3719043", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "109 2 B08 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719043", "GSM3719043: 109 2 B08 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719043", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "109-2-B08-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1184134969.0, 16001572.0, "GSM3719043 r1", "0:74.00 1:0", "A:349230233;C:244528650;G:253057471;T:336773385;N:545230", 74, 0, null, null, 349230233, 244528650, 253057471, 336773385, 545230, "SRX5669645", "SRS4612514", "SRA798477", "GEO", "University of Oxford", 1, 0.88887, null, 0.09304, null, 0.99348, null, 0.98604, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49865, "SRR8883814", "SRX5669644", "SRS4612513", "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", null, "pubmed:32084358", null, "106 2 B05 KOsema3fb tbx18 1 reseq", "GSM3719042", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "106 2 B05 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719042", "GSM3719042: 106 2 B05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719042", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "106-2-B05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1419090881.0, 19189635.0, "GSM3719042 r1", "0:73.95 1:0", "A:373650546;C:329135514;G:344779857;T:370771195;N:753769", 73, 0, null, null, 373650546, 329135514, 344779857, 370771195, 753769, "SRX5669644", "SRS4612513", "SRA798477", "GEO", "University of Oxford", 1, 0.80666, null, 0.39497, null, 0.98307, null, 0.82884, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49866, "SRR8883813", "SRX5669643", "SRS4612512", "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", null, "pubmed:32084358", null, "102 2 B01 KOsema3fb tbx18 1 reseq", "GSM3719041", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "102 2 B01 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719041", "GSM3719041: 102 2 B01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719041", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719041", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "102-2-B01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 792286694.0, 10728522.0, "GSM3719041 r1", "0:73.85 1:0", "A:208005708;C:185723186;G:192254855;T:205724930;N:578015", 73, 0, null, null, 208005708, 185723186, 192254855, 205724930, 578015, "SRX5669643", "SRS4612512", "SRA798477", "GEO", "University of Oxford", 1, 0.83885, null, 0.20822, null, 0.93385, null, 0.55626, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49867, "SRR8883812", "SRX5669642", "SRS4612511", "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", null, "pubmed:32084358", null, "099 2 A10 KOsema3fb tbx18 1 reseq", "GSM3719040", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "099 2 A10 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719040", "GSM3719040: 099 2 A10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719040", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719040", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "099-2-A10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1259856601.0, 17276596.0, "GSM3719040 r1", "0:72.92 1:0", "A:327815757;C:292688430;G:309183926;T:327561592;N:2606896", 72, 0, null, null, 327815757, 292688430, 309183926, 327561592, 2606896, "SRX5669642", "SRS4612511", "SRA798477", "GEO", "University of Oxford", 1, 0.75716, null, 0.21591, null, 0.98545, null, 0.88552, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49868, "SRR8883811", "SRX5669641", "SRS4612510", "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", null, "pubmed:32084358", null, "094 2 A04 KOsema3fb tbx18 1 reseq", "GSM3719039", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "094 2 A04 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719039", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "094-2-A04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1393707010.0, 19037650.0, "GSM3719039 r1", "0:73.21 1:0", "A:419699742;C:277700843;G:287769215;T:406877217;N:1659993", 73, 0, null, null, 419699742, 277700843, 287769215, 406877217, 1659993, "SRX5669641", "SRS4612510", "SRA798477", "GEO", "University of Oxford", 1, 0.89441, null, 0.12858, null, 0.98875, null, 0.97807, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49869, "SRR8883810", "SRX5669640", "SRS4612509", "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", null, "pubmed:32084358", null, "091 2 A01 KOsema3fb tbx18 1 reseq", "GSM3719038", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "091 2 A01 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719038", "GSM3719038: 091 2 A01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719038", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719038", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "091-2-A01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1312071784.0, 17781006.0, "GSM3719038 r1", "0:73.79 1:0", "A:366473328;C:287833987;G:300280345;T:356559257;N:924867", 73, 0, null, null, 366473328, 287833987, 300280345, 356559257, 924867, "SRX5669640", "SRS4612509", "SRA798477", "GEO", "University of Oxford", 1, 0.84829, null, 0.13012, null, 0.99239, null, 0.95627, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49870, "SRR8883809", "SRX5669639", "SRS4612508", "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", null, "pubmed:32084358", null, "089 1 H11 KOsema3fb tbx18 1 reseq", "GSM3719037", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "089 1 H11 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719037", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "089-1-H11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 457617610.0, 6259652.0, "GSM3719037 r1", "0:73.11 1:0", "A:102784836;C:123244653;G:128352318;T:102443570;N:792233", 73, 0, null, null, 102784836, 123244653, 128352318, 102443570, 792233, "SRX5669639", "SRS4612508", "SRA798477", "GEO", "University of Oxford", 1, 0.41215, null, 0.14696, null, 0.99474, null, 0.79701, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49871, "SRR8883808", "SRX5669638", "SRS4612507", "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", null, "pubmed:32084358", null, "088 1 H10 KOsema3fb tbx18 1 reseq", "GSM3719036", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "088 1 H10 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719036", "GSM3719036: 088 1 H10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719036", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719036", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "088-1-H10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1045203718.0, 14235004.0, "GSM3719036 r1", "0:73.42 1:0", "A:245506754;C:275986612;G:284480834;T:238462022;N:767496", 73, 0, null, null, 245506754, 275986612, 284480834, 238462022, 767496, "SRX5669638", "SRS4612507", "SRA798477", "GEO", "University of Oxford", 1, 0.78399, null, 0.27279, null, 0.96171, null, 0.64393, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49872, "SRR8883807", "SRX5669637", "SRS4612506", "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", null, "pubmed:32084358", null, "085 1 H07 KOsema3fb tbx18 1 reseq", "GSM3719035", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "085 1 H07 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719035", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "085-1-H07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 994545532.0, 13515281.0, "GSM3719035 r1", "0:73.59 1:0", "A:251733790;C:239766112;G:249497960;T:252514979;N:1032691", 73, 0, null, null, 251733790, 239766112, 249497960, 252514979, 1032691, "SRX5669637", "SRS4612506", "SRA798477", "GEO", "University of Oxford", 1, 0.76592, null, 0.33384, null, 0.97488, null, 0.6386, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49873, "SRR8883806", "SRX5669636", "SRS4612505", "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", null, "pubmed:32084358", null, "083 1 H05 KOsema3fb tbx18 1 reseq", "GSM3719034", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "083 1 H05 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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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", null, "pubmed:32084358", null, "080 1 H02 KOsema3fb tbx18 1 reseq", "GSM3719033", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "080 1 H02 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719033", "GSM3719033: 080 1 H02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719033", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719033", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "080-1-H02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1858691358.0, 25414284.0, "GSM3719033 r1", "0:73.14 1:0", "A:476963365;C:445987754;G:466752717;T:466112688;N:2874834", 73, 0, null, null, 476963365, 445987754, 466752717, 466112688, 2874834, "SRX5669635", "SRS4612504", "SRA798477", "GEO", "University of Oxford", 1, 0.68992, null, 0.2736, null, 0.982, null, 0.82915, null, 59, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49875, "SRR8883804", "SRX5669634", "SRS4612503", "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", null, "pubmed:32084358", null, "075 1 G09 KOsema3fb tbx18 1 reseq", "GSM3719032", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "075 1 G09 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719032", "GSM3719032: 075 1 G09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719032", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719032", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "075-1-G09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 268112375.0, 3598019.0, "GSM3719032 r1", "0:74.52 1:0", "A:65372074;C:67071915;G:71029798;T:64617919;N:20669", 74, 0, null, null, 65372074, 67071915, 71029798, 64617919, 20669, "SRX5669634", "SRS4612503", "SRA798477", "GEO", "University of Oxford", 1, 0.67884, null, 0.23576, null, 0.98717, null, 0.82171, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49876, "SRR8883803", "SRX5669633", "SRS4612502", "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", null, "pubmed:32084358", null, "071 1 G05 KOsema3fb tbx18 1 reseq", "GSM3719031", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "071 1 G05 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719031", "GSM3719031: 071 1 G05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719031", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719031", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "071-1-G05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 828746401.0, 11302582.0, "GSM3719031 r1", "0:73.32 1:0", "A:229221425;C:183717145;G:190544172;T:224163771;N:1099888", 73, 0, null, null, 229221425, 183717145, 190544172, 224163771, 1099888, "SRX5669633", "SRS4612502", "SRA798477", "GEO", "University of Oxford", 1, 0.81759, null, 0.13538, null, 0.89315, null, 0.45516, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49877, "SRR8883802", "SRX5669631", "SRS4612500", "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", null, "pubmed:32084358", null, "070 1 G04 KOsema3fb tbx18 1 reseq", "GSM3719030", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "070 1 G04 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719030", "GSM3719030: 070 1 G04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719030", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719030", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "070-1-G04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 106414765.0, 1428334.0, "GSM3719030 r1", "0:74.50 1:0", "A:29193564;C:23683625;G:26548630;T:26978197;N:10749", 74, 0, null, null, 29193564, 23683625, 26548630, 26978197, 10749, "SRX5669631", "SRS4612500", "SRA798477", "GEO", "University of Oxford", 1, 0.4816, null, 0.11056, null, 0.99176, null, 0.92847, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49878, "SRR8883801", "SRX5669630", "SRS4612499", "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", null, "pubmed:32084358", null, "063 1 F09 KOsema3fb tbx18 1 reseq", "GSM3719029", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "063 1 F09 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719029", "GSM3719029: 063 1 F09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719029", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719029", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "063-1-F09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1418543217.0, 19449719.0, "GSM3719029 r1", "0:72.93 1:0", "A:337365498;C:374610477;G:384311752;T:320594026;N:1661464", 72, 0, null, null, 337365498, 374610477, 384311752, 320594026, 1661464, "SRX5669630", "SRS4612499", "SRA798477", "GEO", "University of Oxford", 1, 0.72075, null, 0.19017, null, 0.94852, null, 0.65802, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49879, "SRR8883800", "SRX5669629", "SRS4612498", "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", null, "pubmed:32084358", null, "059 1 F05 KOsema3fb tbx18 1 reseq", "GSM3719028", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "059 1 F05 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719028", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "059-1-F05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 628014958.0, 8461681.0, "GSM3719028 r1", "0:74.22 1:0", "A:169712705;C:143325768;G:146633959;T:168144033;N:198493", 74, 0, null, null, 169712705, 143325768, 146633959, 168144033, 198493, "SRX5669629", "SRS4612498", "SRA798477", "GEO", "University of Oxford", 1, 0.88635, null, 0.30859, null, 0.94945, null, 0.51713, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49880, "SRR8883799", "SRX5669628", "SRS4612497", "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", null, "pubmed:32084358", null, "058 1 F04 KOsema3fb tbx18 1 reseq", "GSM3719027", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "058 1 F04 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719027", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "058-1-F04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1132466748.0, 15352198.0, "GSM3719027 r1", "0:73.77 1:0", "A:287483650;C:275728373;G:284236125;T:284105636;N:912964", 73, 0, null, null, 287483650, 275728373, 284236125, 284105636, 912964, "SRX5669628", "SRS4612497", "SRA798477", "GEO", "University of Oxford", 1, 0.85479, null, 0.29074, null, 0.94787, null, 0.64434, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49881, "SRR8883798", "SRX5669627", "SRS4612496", "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", null, "pubmed:32084358", null, "054 1 E12 KOsema3fb tbx18 1 reseq", "GSM3719026", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "054 1 E12 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719026", "GSM3719026: 054 1 E12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719026", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719026", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "054-1-E12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1629595640.0, 22258229.0, "GSM3719026 r1", "0:73.21 1:0", "A:413072064;C:401501367;G:412845503;T:400653209;N:1523497", 73, 0, null, null, 413072064, 401501367, 412845503, 400653209, 1523497, "SRX5669627", "SRS4612496", "SRA798477", "GEO", "University of Oxford", 1, 0.80047, null, 0.25253, null, 0.95489, null, 0.577, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49882, "SRR8883797", "SRX5669626", "SRS4612495", "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", null, "pubmed:32084358", null, "053 1 E11 KOsema3fb tbx18 1 reseq", "GSM3719025", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "053 1 E11 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719025", "GSM3719025: 053 1 E11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719025", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719025", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "053-1-E11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1486706263.0, 20480281.0, "GSM3719025 r1", "0:72.59 1:0", "A:371137003;C:370842438;G:377947483;T:365166253;N:1613086", 72, 0, null, null, 371137003, 370842438, 377947483, 365166253, 1613086, "SRX5669626", "SRS4612495", "SRA798477", "GEO", "University of Oxford", 1, 0.90527, null, 0.12233, null, 0.92535, null, 0.49493, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49883, "SRR8883796", "SRX5669625", "SRS4612494", "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", null, "pubmed:32084358", null, "052 1 E10 KOsema3fb tbx18 1 reseq", "GSM3719024", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "052 1 E10 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719024", "GSM3719024: 052 1 E10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719024", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719024", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "052-1-E10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1081235863.0, 14851741.0, "GSM3719024 r1", "0:72.80 1:0", "A:270268231;C:269602955;G:274380996;T:265977713;N:1005968", 72, 0, null, null, 270268231, 269602955, 274380996, 265977713, 1005968, "SRX5669625", "SRS4612494", "SRA798477", "GEO", "University of Oxford", 1, 0.9403, null, 0.05017, null, 0.90412, null, 0.49703, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49884, "SRR8883795", "SRX5669624", "SRS4612493", "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", null, "pubmed:32084358", null, "046 1 E03 KOsema3fb tbx18 1 reseq", "GSM3719023", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "046 1 E03 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719023", "GSM3719023: 046 1 E03 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719023", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719023", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "046-1-E03-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1601412676.0, 21633821.0, "GSM3719023 r1", "0:74.02 1:0", "A:429878446;C:367923948;G:377956363;T:424839589;N:814330", 74, 0, null, null, 429878446, 367923948, 377956363, 424839589, 814330, "SRX5669624", "SRS4612493", "SRA798477", "GEO", "University of Oxford", 1, 0.87207, null, 0.23243, null, 0.9177, null, 0.55272, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49885, "SRR8883794", "SRX5669623", "SRS4612492", "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", null, "pubmed:32084358", null, "045 1 E02 KOsema3fb tbx18 1 reseq", "GSM3719022", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "045 1 E02 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719022", "GSM3719022: 045 1 E02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719022", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719022", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "045-1-E02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1325652418.0, 18022884.0, "GSM3719022 r1", "0:73.55 1:0", "A:370796542;C:292964387;G:300362786;T:360541988;N:986715", 73, 0, null, null, 370796542, 292964387, 300362786, 360541988, 986715, "SRX5669623", "SRS4612492", "SRA798477", "GEO", "University of Oxford", 1, 0.82878, null, 0.13178, null, 0.99387, null, 0.97164, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49886, "SRR8883793", "SRX5669595", "SRS4612464", "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", null, "pubmed:32084358", null, "042 1 D11 KOsema3fb tbx18 1 reseq", "GSM3719021", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "042 1 D11 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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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", null, "pubmed:32084358", null, "038 1 D06 KOsema3fb tbx18 1 reseq", "GSM3719020", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "038 1 D06 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719020", "GSM3719020: 038 1 D06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719020", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719020", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "038-1-D06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 168156139.0, 2261594.0, "GSM3719020 r1", "0:74.35 1:0", "A:42354992;C:41900555;G:44340628;T:39432087;N:127877", 74, 0, null, null, 42354992, 41900555, 44340628, 39432087, 127877, "SRX5669594", "SRS4612463", "SRA798477", "GEO", "University of Oxford", 1, 0.60767, null, 0.21853, null, 0.9903, null, 0.79842, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49888, "SRR8883791", "SRX5669593", "SRS4612462", "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", null, "pubmed:32084358", null, "033 1 D01 KOsema3fb tbx18 1 reseq", "GSM3719019", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "033 1 D01 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719019", "GSM3719019: 033 1 D01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719019", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719019", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "033-1-D01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1805852084.0, 24752177.0, "GSM3719019 r1", "0:72.96 1:0", "A:484272872;C:416872457;G:427392429;T:474646299;N:2668027", 72, 0, null, null, 484272872, 416872457, 427392429, 474646299, 2668027, "SRX5669593", "SRS4612462", "SRA798477", "GEO", "University of Oxford", 1, 0.86769, null, 0.24446, null, 0.90954, null, 0.52112, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49889, "SRR8883790", "SRX5669592", "SRS4612461", "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", null, "pubmed:32084358", null, "031 1 C11 KOsema3fb tbx18 1 reseq", "GSM3719018", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "031 1 C11 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719018", "GSM3719018: 031 1 C11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719018", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719018", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "031-1-C11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 258591680.0, 3472457.0, "GSM3719018 r1", "0:74.47 1:0", "A:64790229;C:64970309;G:69416663;T:59350946;N:63533", 74, 0, null, null, 64790229, 64970309, 69416663, 59350946, 63533, "SRX5669592", "SRS4612461", "SRA798477", "GEO", "University of Oxford", 1, 0.6005, null, 0.17126, null, 0.99139, null, 0.81853, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49890, "SRR8883789", "SRX5669591", "SRS4612460", "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", null, "pubmed:32084358", null, "027 1 C06 KOsema3fb tbx18 1 reseq", "GSM3719017", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "027 1 C06 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719017", "GSM3719017: 027 1 C06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719017", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719017", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "027-1-C06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1296475193.0, 17694501.0, "GSM3719017 r1", "0:73.27 1:0", "A:351327244;C:293439849;G:302900890;T:347251212;N:1555998", 73, 0, null, null, 351327244, 293439849, 302900890, 347251212, 1555998, "SRX5669591", "SRS4612460", "SRA798477", "GEO", "University of Oxford", 1, 0.85074, null, 0.26491, null, 0.90749, null, 0.56504, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49891, "SRR8883788", "SRX5669590", "SRS4612459", "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", null, "pubmed:32084358", null, "026 1 C05 KOsema3fb tbx18 1 reseq", "GSM3719016", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "026 1 C05 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719016", "GSM3719016: 026 1 C05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719016", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719016", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "026-1-C05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 284767981.0, 3826742.0, "GSM3719016 r1", "0:74.42 1:0", "A:72059849;C:70126842;G:73586073;T:68935800;N:59417", 74, 0, null, null, 72059849, 70126842, 73586073, 68935800, 59417, "SRX5669590", "SRS4612459", "SRA798477", "GEO", "University of Oxford", 1, 0.64774, null, 0.40257, null, 0.98926, null, 0.81073, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49892, "SRR8883787", "SRX5669589", "SRS4612458", "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", null, "pubmed:32084358", null, "023 1 C02 KOsema3fb tbx18 1 reseq", "GSM3719015", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "023 1 C02 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719015", "GSM3719015: 023 1 C02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719015", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "023-1-C02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 350095216.0, 4702156.0, "GSM3719015 r1", "0:74.45 1:0", "A:86568719;C:87778353;G:93408696;T:82295750;N:43698", 74, 0, null, null, 86568719, 87778353, 93408696, 82295750, 43698, "SRX5669589", "SRS4612458", "SRA798477", "GEO", "University of Oxford", 1, 0.68061, null, 0.26106, null, 0.99308, null, 0.78108, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49893, "SRR8883786", "SRX5669588", "SRS4612457", "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", null, "pubmed:32084358", null, "021 1 B12 KOsema3fb tbx18 1 reseq", "GSM3719014", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "021 1 B12 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719014", "GSM3719014: 021 1 B12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719014", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719014", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "021-1-B12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 244139057.0, 3276020.0, "GSM3719014 r1", "0:74.52 1:0", "A:57869172;C:62768357;G:66137806;T:57351114;N:12608", 74, 0, null, null, 57869172, 62768357, 66137806, 57351114, 12608, "SRX5669588", "SRS4612457", "SRA798477", "GEO", "University of Oxford", 1, 0.82069, null, 0.30044, null, 0.98835, null, 0.7106, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49894, "SRR8883785", "SRX5669587", "SRS4612456", "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", null, "pubmed:32084358", null, "013 1 B03 KOsema3fb tbx18 1 reseq", "GSM3719013", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "013 1 B03 KOsema3fb tbx18 1 reseq", "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", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. 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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. 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