metadata: run_metadata: 735 rows where experiment.library_layout = "PAIRED", technology = "smartseq" and tissue

735 rows where experiment.library_layout = "PAIRED", technology = "smartseq" and tissue_curation = "Heart"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
4359	4359	ERR1427424	ERX1497956	ERS1183258	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#91	SAMEA4012148	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012148\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#91\|broker name:ArrayExpress\|common name:zebrafish\|fsc:25859\|gfp:119\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#91\|ssc:10090\|tissue:Heart\|well:C12							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#91	LCK 7#91	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 25859:fsc\|Experimental Factor: 10090:ssc\|Experimental Factor: 119:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_91_mod.bam LCK_7_91.cram	bam cram			E MTAB 4617:LCK 7#91	0:125 1:125	A:115117295;C:110480558;G:102056870;T:121829131;N:52646	125	125	115117295	110480558	102056870	121829131	52646	ERX1497956		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.2053	0.20024	0.06111	0.05989	0.98019	0.98058	0.56103	0.56868	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4360	4360	ERR1427423	ERX1497955	ERS1183257	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#90	SAMEA4012147	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012147\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#90\|broker name:ArrayExpress\|common name:zebrafish\|fsc:22987\|gfp:178\|individual:2\|pi:6\|plate:7\|sample name:E MTAB 4617:LCK 7#90\|ssc:6327\|tissue:Heart\|well:B12							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#90	LCK 7#90	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 22987:fsc\|Experimental Factor: 6327:ssc\|Experimental Factor: 178:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_90_mod.bam LCK_7_90.cram	bam cram			E MTAB 4617:LCK 7#90	0:125 1:125	A:106342222;C:98049090;G:91971650;T:111243138;N:46400	125	125	106342222	98049090	91971650	111243138	46400	ERX1497955		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.2785	0.27322	0.08361	0.08291	0.97619	0.97703	0.60537	0.61379	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4361	4361	ERR1427422	ERX1497954	ERS1183256	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#9	SAMEA4012146	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012146\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#9\|broker name:ArrayExpress\|common name:zebrafish\|fsc:24861\|gfp:531\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#9\|ssc:5852\|tissue:Heart\|well:A2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#9	LCK 7#9	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 24861:fsc\|Experimental Factor: 5852:ssc\|Experimental Factor: 531:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_9_mod.bam LCK_7_9.cram	bam cram			E MTAB 4617:LCK 7#9	0:125 1:125	A:99732231;C:96455828;G:89233454;T:105851298;N:47439	125	125	99732231	96455828	89233454	105851298	47439	ERX1497954		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.21894	0.21406	0.0599	0.05904	0.97861	0.97877	0.57755	0.57546	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4362	4362	ERR1427421	ERX1497953	ERS1183255	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#89	SAMEA4012145	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012145\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#89\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26923\|gfp:664\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#89\|ssc:7976\|tissue:Heart\|well:A12							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#89	LCK 7#89	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26923:fsc\|Experimental Factor: 7976:ssc\|Experimental Factor: 664:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_89_mod.bam LCK_7_89.cram	bam cram			E MTAB 4617:LCK 7#89	0:125 1:125	A:53847121;C:51852010;G:47816940;T:57047962;N:23717	125	125	53847121	51852010	47816940	57047962	23717	ERX1497953		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.22382	0.21939	0.05208	0.05177	0.97952	0.97979	0.49483	0.59346	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4368	4368	ERR1427415	ERX1497947	ERS1183249	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#83	SAMEA4012139	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012139\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#83\|broker name:ArrayExpress\|common name:zebrafish\|fsc:23855\|gfp:97\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#83\|ssc:7394\|tissue:Heart\|well:C11							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#83	LCK 7#83	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 23855:fsc\|Experimental Factor: 7394:ssc\|Experimental Factor: 97:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_83_mod.bam LCK_7_83.cram	bam cram			E MTAB 4617:LCK 7#83	0:125 1:125	A:73686338;C:69380167;G:63301440;T:77949626;N:35429	125	125	73686338	69380167	63301440	77949626	35429	ERX1497947		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.1643	0.16094	0.06354	0.06267	0.98526	0.98581	0.60921	0.60841	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4369	4369	ERR1427414	ERX1497946	ERS1183248	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#82	SAMEA4012138	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012138\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#82\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27473\|gfp:554\|individual:2\|pi:3\|plate:7\|sample name:E MTAB 4617:LCK 7#82\|ssc:9625\|tissue:Heart\|well:B11							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#82	LCK 7#82	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27473:fsc\|Experimental Factor: 9625:ssc\|Experimental Factor: 554:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_82_mod.bam LCK_7_82.cram	bam cram			E MTAB 4617:LCK 7#82	0:125 1:125	A:132306808;C:126337107;G:118115874;T:139760194;N:65267	125	125	132306808	126337107	118115874	139760194	65267	ERX1497946		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.18655	0.18247	0.05663	0.05588	0.97916	0.97918	0.57019	0.56851	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4370	4370	ERR1427413	ERX1497945	ERS1183247	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#81	SAMEA4012137	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012137\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#81\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26381\|gfp:492\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#81\|ssc:6369\|tissue:Heart\|well:A11							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#81	LCK 7#81	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26381:fsc\|Experimental Factor: 6369:ssc\|Experimental Factor: 492:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_81_mod.bam LCK_7_81.cram	bam cram			E MTAB 4617:LCK 7#81	0:125 1:125	A:49752056;C:47569625;G:43787172;T:52848426;N:21471	125	125	49752056	47569625	43787172	52848426	21471	ERX1497945		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.18831	0.18533	0.05553	0.05564	0.98076	0.98147	0.55231	0.5582	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4377	4377	ERR1427406	ERX1497938	ERS1183240	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#75	SAMEA4012130	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012130\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#75\|broker name:ArrayExpress\|common name:zebrafish\|fsc:29804\|gfp:381\|individual:2\|pi:3\|plate:7\|sample name:E MTAB 4617:LCK 7#75\|ssc:9855\|tissue:Heart\|well:C10							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#75	LCK 7#75	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 29804:fsc\|Experimental Factor: 9855:ssc\|Experimental Factor: 381:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_75_mod.bam LCK_7_75.cram	bam cram			E MTAB 4617:LCK 7#75	0:125 1:125	A:215270392;C:173814423;G:161953517;T:222035470;N:96448	125	125	215270392	173814423	161953517	222035470	96448	ERX1497938		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.40731	0.4045	0.14845	0.14768	0.97908	0.97906	0.59339	0.61288	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4378	4378	ERR1427405	ERX1497937	ERS1183239	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#74	SAMEA4012129	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012129\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:15Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#74\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27947\|gfp:352\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#74\|ssc:7917\|tissue:Heart\|well:B10							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#74	LCK 7#74	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27947:fsc\|Experimental Factor: 7917:ssc\|Experimental Factor: 352:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_74_mod.bam LCK_7_74.cram	bam cram			E MTAB 4617:LCK 7#74	0:125 1:125	A:123931531;C:111767107;G:106439636;T:128665381;N:58095	125	125	123931531	111767107	106439636	128665381	58095	ERX1497937		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.24486	0.2405	0.06375	0.06316	0.97845	0.97938	0.55948	0.55443	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4379	4379	ERR1427404	ERX1497936	ERS1183238	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#73	SAMEA4012128	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012128\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#73\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27976\|gfp:511\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#73\|ssc:9269\|tissue:Heart\|well:A10							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#73	LCK 7#73	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27976:fsc\|Experimental Factor: 9269:ssc\|Experimental Factor: 511:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_73_mod.bam LCK_7_73.cram	bam cram			E MTAB 4617:LCK 7#73	0:125 1:125	A:47487658;C:44369011;G:41797745;T:49759850;N:22236	125	125	47487658	44369011	41797745	49759850	22236	ERX1497936		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.20054	0.19572	0.06216	0.06174	0.98141	0.98165	0.57621	0.56697	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4386	4386	ERR1427397	ERX1497929	ERS1183231	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#67	SAMEA4012121	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012121\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#67\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27129\|gfp:522\|individual:2\|pi:3\|plate:7\|sample name:E MTAB 4617:LCK 7#67\|ssc:7035\|tissue:Heart\|well:C9							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#67	LCK 7#67	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27129:fsc\|Experimental Factor: 7035:ssc\|Experimental Factor: 522:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_67_mod.bam LCK_7_67.cram	bam cram			E MTAB 4617:LCK 7#67	0:125 1:125	A:211181074;C:167361986;G:152479010;T:214248000;N:87930	125	125	211181074	167361986	152479010	214248000	87930	ERX1497929		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.35381	0.35317	0.14449	0.14491	0.97865	0.97897	0.57854	0.58021	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4387	4387	ERR1427396	ERX1497928	ERS1183230	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#66	SAMEA4012120	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012120\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#66\|broker name:ArrayExpress\|common name:zebrafish\|fsc:23015\|gfp:48\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#66\|ssc:6562\|tissue:Heart\|well:B9							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#66	LCK 7#66	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 23015:fsc\|Experimental Factor: 6562:ssc\|Experimental Factor: 48:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_66_mod.bam LCK_7_66.cram	bam cram			E MTAB 4617:LCK 7#66	0:125 1:125	A:122494933;C:109921862;G:103257549;T:125665684;N:56722	125	125	122494933	109921862	103257549	125665684	56722	ERX1497928		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.18714	0.18418	0.0608	0.06082	0.9839	0.98441	0.60081	0.59623	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4388	4388	ERR1427395	ERX1497927	ERS1183229	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#65	SAMEA4012119	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012119\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#65\|broker name:ArrayExpress\|common name:zebrafish\|fsc:23857\|gfp:308\|individual:2\|pi:4\|plate:7\|sample name:E MTAB 4617:LCK 7#65\|ssc:4888\|tissue:Heart\|well:A9							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#65	LCK 7#65	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 23857:fsc\|Experimental Factor: 4888:ssc\|Experimental Factor: 308:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_65_mod.bam LCK_7_65.cram	bam cram			E MTAB 4617:LCK 7#65	0:125 1:125	A:96259909;C:89965165;G:84222055;T:99868995;N:43376	125	125	96259909	89965165	84222055	99868995	43376	ERX1497927		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.25582	0.25073	0.07651	0.07583	0.98044	0.98106	0.67809	0.67977	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4395	4395	ERR1427388	ERX1497920	ERS1183222	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#59	SAMEA4012112	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012112\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#59\|broker name:ArrayExpress\|common name:zebrafish\|fsc:20472\|gfp:126\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#59\|ssc:10300\|tissue:Heart\|well:C8							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#59	LCK 7#59	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 20472:fsc\|Experimental Factor: 10300:ssc\|Experimental Factor: 126:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_59_mod.bam LCK_7_59.cram	bam cram			E MTAB 4617:LCK 7#59	0:125 1:125	A:134247255;C:121203898;G:112067297;T:140566781;N:62269	125	125	134247255	121203898	112067297	140566781	62269	ERX1497920		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.27548	0.27103	0.09818	0.09707	0.97861	0.97922	0.54371	0.57755	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4396	4396	ERR1427387	ERX1497919	ERS1183221	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#58	SAMEA4012111	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012111\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#58\|broker name:ArrayExpress\|common name:zebrafish\|fsc:30361\|gfp:242\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#58\|ssc:7886\|tissue:Heart\|well:B8							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#58	LCK 7#58	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 30361:fsc\|Experimental Factor: 7886:ssc\|Experimental Factor: 242:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_58_mod.bam LCK_7_58.cram	bam cram			E MTAB 4617:LCK 7#58	0:125 1:125	A:165043952;C:161634321;G:152303735;T:174314970;N:75022	125	125	165043952	161634321	152303735	174314970	75022	ERX1497919		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.16408	0.16208	0.06572	0.06486	0.97918	0.97922	0.52752	0.52567	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4397	4397	ERR1427386	ERX1497918	ERS1183220	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#57	SAMEA4012110	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012110\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#57\|broker name:ArrayExpress\|common name:zebrafish\|fsc:30152\|gfp:130\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#57\|ssc:6428\|tissue:Heart\|well:A8							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#57	LCK 7#57	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 30152:fsc\|Experimental Factor: 6428:ssc\|Experimental Factor: 130:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_57_mod.bam LCK_7_57.cram	bam cram			E MTAB 4617:LCK 7#57	0:125 1:125	A:81845074;C:82172065;G:76757417;T:87625766;N:38678	125	125	81845074	82172065	76757417	87625766	38678	ERX1497918		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.11381	0.11124	0.03217	0.03208	0.98253	0.98299	0.58282	0.58741	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4403	4403	ERR1427380	ERX1497912	ERS1183214	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#51	SAMEA4012104	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012104\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#51\|broker name:ArrayExpress\|common name:zebrafish\|fsc:28503\|gfp:536\|individual:2\|pi:3\|plate:7\|sample name:E MTAB 4617:LCK 7#51\|ssc:5896\|tissue:Heart\|well:C7							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#51	LCK 7#51	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 28503:fsc\|Experimental Factor: 5896:ssc\|Experimental Factor: 536:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_51_mod.bam LCK_7_51.cram	bam cram			E MTAB 4617:LCK 7#51	0:125 1:125	A:68083321;C:57560520;G:49834107;T:71348826;N:28226	125	125	68083321	57560520	49834107	71348826	28226	ERX1497912		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.22734	0.22491	0.09383	0.09424	0.98019	0.98127	0.60101	0.59084	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4404	4404	ERR1427379	ERX1497911	ERS1183213	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#50	SAMEA4012103	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012103\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#50\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27497\|gfp:574\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#50\|ssc:8308\|tissue:Heart\|well:B7							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#50	LCK 7#50	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27497:fsc\|Experimental Factor: 8308:ssc\|Experimental Factor: 574:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_50_mod.bam LCK_7_50.cram	bam cram			E MTAB 4617:LCK 7#50	0:125 1:125	A:200436684;C:191639110;G:173623845;T:213497904;N:94207	125	125	200436684	191639110	173623845	213497904	94207	ERX1497911		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.08784	0.08742	0.04628	0.04599	0.98784	0.98823	0.5655	0.56486	125	125	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4406	4406	ERR1427377	ERX1497909	ERS1183211	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#49	SAMEA4012101	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012101\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#49\|broker name:ArrayExpress\|common name:zebrafish\|fsc:30443\|gfp:456\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#49\|ssc:8077\|tissue:Heart\|well:A7							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#49	LCK 7#49	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 30443:fsc\|Experimental Factor: 8077:ssc\|Experimental Factor: 456:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_49_mod.bam LCK_7_49.cram	bam cram			E MTAB 4617:LCK 7#49	0:125 1:125	A:96840239;C:94376256;G:85197984;T:104185788;N:45483	125	125	96840239	94376256	85197984	104185788	45483	ERX1497909		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.17039	0.16705	0.05666	0.05595	0.98133	0.98196	0.59139	0.59279	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4412	4412	ERR1427371	ERX1497903	ERS1183205	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#43	SAMEA4012095	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012095\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#43\|broker name:ArrayExpress\|common name:zebrafish\|fsc:21270\|gfp:120\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#43\|ssc:7066\|tissue:Heart\|well:C6							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#43	LCK 7#43	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 21270:fsc\|Experimental Factor: 7066:ssc\|Experimental Factor: 120:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_43_mod.bam LCK_7_43.cram	bam cram			E MTAB 4617:LCK 7#43	0:125 1:125	A:95132366;C:87995738;G:81475905;T:100137372;N:45119	125	125	95132366	87995738	81475905	100137372	45119	ERX1497903		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.21518	0.21129	0.06702	0.06612	0.97887	0.97944	0.5799	0.57556	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4413	4413	ERR1427370	ERX1497902	ERS1183204	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#42	SAMEA4012094	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012094\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#42\|broker name:ArrayExpress\|common name:zebrafish\|fsc:19274\|gfp:88\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#42\|ssc:6422\|tissue:Heart\|well:B6							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#42	LCK 7#42	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 19274:fsc\|Experimental Factor: 6422:ssc\|Experimental Factor: 88:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_42_mod.bam LCK_7_42.cram	bam cram			E MTAB 4617:LCK 7#42	0:125 1:125	A:45015627;C:40505684;G:37787157;T:46787414;N:20618	125	125	45015627	40505684	37787157	46787414	20618	ERX1497902		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.14859	0.1471	0.0553	0.05579	0.98058	0.98151	0.57477	0.57968	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4414	4414	ERR1427369	ERX1497901	ERS1183203	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#41	SAMEA4012093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012093\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:14Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#41\|broker name:ArrayExpress\|common name:zebrafish\|fsc:20292\|gfp:198\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#41\|ssc:6233\|tissue:Heart\|well:A6							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#41	LCK 7#41	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 20292:fsc\|Experimental Factor: 6233:ssc\|Experimental Factor: 198:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_41_mod.bam LCK_7_41.cram	bam cram			E MTAB 4617:LCK 7#41	0:125 1:125	A:89502636;C:89074499;G:83078909;T:95568395;N:39311	125	125	89502636	89074499	83078909	95568395	39311	ERX1497901		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.09383	0.09131	0.02199	0.02189	0.98569	0.98577	0.58856	0.59531	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4421	4421	ERR1427362	ERX1497894	ERS1183196	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#35	SAMEA4012086	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012086\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#35\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26079\|gfp:93\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#35\|ssc:4930\|tissue:Heart\|well:C5							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#35	LCK 7#35	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26079:fsc\|Experimental Factor: 4930:ssc\|Experimental Factor: 93:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_35_mod.bam LCK_7_35.cram	bam cram			E MTAB 4617:LCK 7#35	0:125 1:125	A:139844227;C:137312069;G:126169914;T:149207606;N:69934	125	125	139844227	137312069	126169914	149207606	69934	ERX1497894		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.19648	0.19308	0.05501	0.05463	0.98149	0.982	0.60289	0.60804	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4422	4422	ERR1427361	ERX1497893	ERS1183195	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#34	SAMEA4012085	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012085\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#34\|broker name:ArrayExpress\|common name:zebrafish\|fsc:25615\|gfp:81\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#34\|ssc:5934\|tissue:Heart\|well:B5							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#34	LCK 7#34	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 25615:fsc\|Experimental Factor: 5934:ssc\|Experimental Factor: 81:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_34_mod.bam LCK_7_34.cram	bam cram			E MTAB 4617:LCK 7#34	0:125 1:125	A:134481938;C:127574886;G:118538403;T:142102568;N:61455	125	125	134481938	127574886	118538403	142102568	61455	ERX1497893		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.19982	0.1964	0.06657	0.0662	0.98092	0.98119	0.59089	0.58445	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4423	4423	ERR1427360	ERX1497892	ERS1183194	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#33	SAMEA4012084	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012084\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#33\|broker name:ArrayExpress\|common name:zebrafish\|fsc:28221\|gfp:414\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#33\|ssc:5341\|tissue:Heart\|well:A5							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#33	LCK 7#33	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 28221:fsc\|Experimental Factor: 5341:ssc\|Experimental Factor: 414:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_33_mod.bam LCK_7_33.cram	bam cram			E MTAB 4617:LCK 7#33	0:125 1:125	A:93220735;C:94390552;G:86770054;T:100705096;N:43313	125	125	93220735	94390552	86770054	100705096	43313	ERX1497892		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.09686	0.09522	0.02902	0.02873	0.98228	0.98279	0.54935	0.54646	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4427	4427	ERR1427356	ERX1497888	ERS1183190	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#3	SAMEA4012080	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012080\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#3\|broker name:ArrayExpress\|common name:zebrafish\|fsc:25075\|gfp:108\|individual:2\|pi:4\|plate:7\|sample name:E MTAB 4617:LCK 7#3\|ssc:7682\|tissue:Heart\|well:C1							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#3	LCK 7#3	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 25075:fsc\|Experimental Factor: 7682:ssc\|Experimental Factor: 108:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_3_mod.bam LCK_7_3.cram	bam cram			E MTAB 4617:LCK 7#3	0:125 1:125	A:58493174;C:54183075;G:50060440;T:61036959;N:28352	125	125	58493174	54183075	50060440	61036959	28352	ERX1497888		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.15762	0.1526	0.04924	0.04785	0.97906	0.97966	0.55641	0.55037	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4430	4430	ERR1427353	ERX1497885	ERS1183187	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#27	SAMEA4012077	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012077\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#27\|broker name:ArrayExpress\|common name:zebrafish\|fsc:29359\|gfp:456\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#27\|ssc:10950\|tissue:Heart\|well:C4							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#27	LCK 7#27	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 29359:fsc\|Experimental Factor: 10950:ssc\|Experimental Factor: 456:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_27_mod.bam LCK_7_27.cram	bam cram			E MTAB 4617:LCK 7#27	0:125 1:125	A:116175271;C:110956295;G:101584573;T:123371066;N:51045	125	125	116175271	110956295	101584573	123371066	51045	ERX1497885		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.25865	0.25265	0.08041	0.07902	0.97601	0.97595	0.55457	0.55357	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4431	4431	ERR1427352	ERX1497884	ERS1183186	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#26	SAMEA4012076	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012076\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#26\|broker name:ArrayExpress\|common name:zebrafish\|fsc:25525\|gfp:162\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#26\|ssc:5861\|tissue:Heart\|well:B4							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#26	LCK 7#26	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 25525:fsc\|Experimental Factor: 5861:ssc\|Experimental Factor: 162:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_26_mod.bam LCK_7_26.cram	bam cram			E MTAB 4617:LCK 7#26	0:125 1:125	A:84022783;C:79751329;G:73366671;T:88820379;N:40588	125	125	84022783	79751329	73366671	88820379	40588	ERX1497884		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.13334	0.13062	0.04098	0.04053	0.98405	0.98439	0.43923	0.56542	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4432	4432	ERR1427351	ERX1497883	ERS1183185	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#25	SAMEA4012075	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012075\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#25\|broker name:ArrayExpress\|common name:zebrafish\|fsc:28284\|gfp:515\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#25\|ssc:8791\|tissue:Heart\|well:A4							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#25	LCK 7#25	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 28284:fsc\|Experimental Factor: 8791:ssc\|Experimental Factor: 515:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_25_mod.bam LCK_7_25.cram	bam cram			E MTAB 4617:LCK 7#25	0:125 1:125	A:93291373;C:90572911;G:83617400;T:99965116;N:42450	125	125	93291373	90572911	83617400	99965116	42450	ERX1497883		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.22059	0.21595	0.06285	0.06239	0.97739	0.97755	0.60441	0.5941	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4438	4438	ERR1427345	ERX1497877	ERS1183179	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#2	SAMEA4012069	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012069\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#2\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26546\|gfp:74\|individual:2\|pi:4\|plate:7\|sample name:E MTAB 4617:LCK 7#2\|ssc:5884\|tissue:Heart\|well:B1							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#2	LCK 7#2	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26546:fsc\|Experimental Factor: 5884:ssc\|Experimental Factor: 74:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_2_mod.bam LCK_7_2.cram	bam cram			E MTAB 4617:LCK 7#2	0:125 1:125	A:50810642;C:45505266;G:42437381;T:52252338;N:22373	125	125	50810642	45505266	42437381	52252338	22373	ERX1497877		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.13878	0.13634	0.03454	0.03422	0.98179	0.98238	0.53282	0.54119	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4439	4439	ERR1427344	ERX1497876	ERS1183178	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#19	SAMEA4012068	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012068\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#19\|broker name:ArrayExpress\|common name:zebrafish\|fsc:27939\|gfp:269\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#19\|ssc:7748\|tissue:Heart\|well:C3							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#19	LCK 7#19	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 27939:fsc\|Experimental Factor: 7748:ssc\|Experimental Factor: 269:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_19_mod.bam LCK_7_19.cram	bam cram			E MTAB 4617:LCK 7#19	0:125 1:125	A:123448577;C:117648440;G:109679332;T:127799152;N:59249	125	125	123448577	117648440	109679332	127799152	59249	ERX1497876		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.20997	0.20449	0.04702	0.04606	0.98013	0.98068	0.58105	0.58018	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4440	4440	ERR1427343	ERX1497875	ERS1183177	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#18	SAMEA4012067	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012067\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#18\|broker name:ArrayExpress\|common name:zebrafish\|fsc:23930\|gfp:89\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#18\|ssc:7002\|tissue:Heart\|well:B3							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#18	LCK 7#18	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 23930:fsc\|Experimental Factor: 7002:ssc\|Experimental Factor: 89:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_18_mod.bam LCK_7_18.cram	bam cram			E MTAB 4617:LCK 7#18	0:125 1:125	A:116722795;C:108761302;G:102297772;T:120311653;N:53978	125	125	116722795	108761302	102297772	120311653	53978	ERX1497875		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.17035	0.16607	0.04165	0.04071	0.98275	0.98315	0.57334	0.56296	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4441	4441	ERR1427342	ERX1497874	ERS1183176	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#17	SAMEA4012066	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012066\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#17\|broker name:ArrayExpress\|common name:zebrafish\|fsc:19157\|gfp:158\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#17\|ssc:7404\|tissue:Heart\|well:A3							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#17	LCK 7#17	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 19157:fsc\|Experimental Factor: 7404:ssc\|Experimental Factor: 158:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_17_mod.bam LCK_7_17.cram	bam cram			E MTAB 4617:LCK 7#17	0:125 1:125	A:114273839;C:106761242;G:100217178;T:118680369;N:52122	125	125	114273839	106761242	100217178	118680369	52122	ERX1497874		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.26249	0.25596	0.06917	0.06842	0.9737	0.97425	0.59255	0.59411	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4447	4447	ERR1427336	ERX1497868	ERS1183170	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#11	SAMEA4012060	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012060\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#11\|broker name:ArrayExpress\|common name:zebrafish\|fsc:23053\|gfp:148\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#11\|ssc:3985\|tissue:Heart\|well:C2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#11	LCK 7#11	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 23053:fsc\|Experimental Factor: 3985:ssc\|Experimental Factor: 148:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_11_mod.bam LCK_7_11.cram	bam cram			E MTAB 4617:LCK 7#11	0:125 1:125	A:94603298;C:90252097;G:83046109;T:99899414;N:44332	125	125	94603298	90252097	83046109	99899414	44332	ERX1497868		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.24988	0.24291	0.07669	0.07453	0.97857	0.97901	0.52877	0.53451	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4448	4448	ERR1427335	ERX1497867	ERS1183169	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#10	SAMEA4012059	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012059\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#10\|broker name:ArrayExpress\|common name:zebrafish\|fsc:26350\|gfp:91\|individual:2\|pi:2\|plate:7\|sample name:E MTAB 4617:LCK 7#10\|ssc:5717\|tissue:Heart\|well:B2							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#10	LCK 7#10	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 26350:fsc\|Experimental Factor: 5717:ssc\|Experimental Factor: 91:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_10_mod.bam LCK_7_10.cram	bam cram			E MTAB 4617:LCK 7#10	0:125 1:125	A:136048498;C:130651014;G:121379521;T:142822578;N:64889	125	125	136048498	130651014	121379521	142822578	64889	ERX1497867		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.14978	0.14551	0.04586	0.0445	0.98516	0.98559	0.55716	0.54592	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
4449	4449	ERR1427334	ERX1497866	ERS1183168	ERP015799	PRJEB14175	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E-MTAB-4617	Transcriptome Analysis	Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2016 05 26\|ArrayExpress:E MTAB 4617		Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	LCK 7#1	SAMEA4012058	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics	ENA first public:2016 12 01\|ENA last update:2016 05 26\|External Id:SAMEA4012058\|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics\|INSDC first public:2016 12 01T17:01:24Z\|INSDC last update:2016 05 26T17:59:13Z\|INSDC status:public\|Submitter Id:E MTAB 4617:LCK 7#1\|broker name:ArrayExpress\|common name:zebrafish\|fsc:22006\|gfp:487\|individual:2\|pi:1\|plate:7\|sample name:E MTAB 4617:LCK 7#1\|ssc:6542\|tissue:Heart\|well:A1							Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	E MTAB 4617:LCK 7#1	LCK 7#1	Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed.	Experimental Factor: Heart:tissue\|Experimental Factor: 22006:fsc\|Experimental Factor: 6542:ssc\|Experimental Factor: 487:gfp	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP015799	Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish	ENA FIRST PUBLIC:2016 12 01\|ENA LAST UPDATE:2018 11 16	LCK_7_1_mod.bam LCK_7_1.cram	bam cram			E MTAB 4617:LCK 7#1	0:125 1:125	A:128250593;C:122748202;G:114418508;T:135400263;N:59934	125	125	128250593	122748202	114418508	135400263	59934	ERX1497866		ERA631093	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics\|European Nucleotide Archive	2	0.15168	0.14994	0.07129	0.07092	0.98202	0.98163	0.61662	0.63065	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	unknown	sc	single_cell_plate	smartseq	Switzerland	2016-05-26	Adult	Adult	Heart	Cardiovascular System
49899	49899	SRR8883780	SRX5669581	SRS4612450	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		148 2 E12 KOcxcl12a 6	GSM3719008		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	148 2 E12 KOcxcl12a 6	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719008	GSM3719008: 148 2 E12 KOcxcl12a 6; Danio rerio; RNA Seq	GSM3719008		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719008	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			148-2-E12-KOcxcl12a-6_all_lanes_R1.fastq.gz 148-2-E12-KOcxcl12a-6_all_lanes_R2.fastq.gz	fastq fastq	99264702.0	667893.0	GSM3719008 r1	0:74.31 1:74.31	A:24182760;C:25303406;G:25958104;T:23740781;N:79651	74	74	24182760	25303406	25958104	23740781	79651	SRX5669581	SRS4612450	SRA798477	GEO	University of Oxford	2	0.91963	0.91707	0.25543	0.25598	0.77885	0.78526	0.64562	0.65202	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49900	49900	SRR8883779	SRX5669580	SRS4612449	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		147 2 E11 KOcxcl12a 5	GSM3719007		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	147 2 E11 KOcxcl12a 5	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719007	GSM3719007: 147 2 E11 KOcxcl12a 5; Danio rerio; RNA Seq	GSM3719007		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719007	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			147-2-E11-KOcxcl12a-5_all_lanes_R2.fastq.gz 147-2-E11-KOcxcl12a-5_all_lanes_R1.fastq.gz	fastq fastq	106939236.0	718050.0	GSM3719007 r1	0:74.47 1:74.47	A:25999817;C:27345657;G:27993944;T:25531888;N:67930	74	74	25999817	27345657	27993944	25531888	67930	SRX5669580	SRS4612449	SRA798477	GEO	University of Oxford	2	0.93397	0.9304	0.28472	0.28391	0.78995	0.79377	0.63586	0.63708	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49901	49901	SRR8883778	SRX5669579	SRS4612448	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		146 2 E10 KOcxcl12a 4	GSM3719006		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	146 2 E10 KOcxcl12a 4	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719006	GSM3719006: 146 2 E10 KOcxcl12a 4; Danio rerio; RNA Seq	GSM3719006		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719006	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			146-2-E10-KOcxcl12a-4_all_lanes_R2.fastq.gz 146-2-E10-KOcxcl12a-4_all_lanes_R1.fastq.gz	fastq fastq	128269313.0	868280.0	GSM3719006 r1	0:73.86 1:73.86	A:31007547;C:32979513;G:33717602;T:30425592;N:139059	73	73	31007547	32979513	33717602	30425592	139059	SRX5669579	SRS4612448	SRA798477	GEO	University of Oxford	2	0.92669	0.92674	0.24854	0.24879	0.78727	0.79164	0.64818	0.65414	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49902	49902	SRR8883777	SRX5669578	SRS4612447	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		145 2 E09 KOcxcl12a 3	GSM3719005		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	145 2 E09 KOcxcl12a 3	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719005	GSM3719005: 145 2 E09 KOcxcl12a 3; Danio rerio; RNA Seq	GSM3719005		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719005	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			145-2-E09-KOcxcl12a-3_all_lanes_R1.fastq.gz 145-2-E09-KOcxcl12a-3_all_lanes_R2.fastq.gz	fastq fastq	121755625.0	825242.0	GSM3719005 r1	0:73.77 1:73.77	A:30614648;C:30136581;G:30787289;T:30068959;N:148148	73	73	30614648	30136581	30787289	30068959	148148	SRX5669578	SRS4612447	SRA798477	GEO	University of Oxford	2	0.91445	0.91357	0.3015	0.30027	0.7781	0.78186	0.63683	0.63951	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49903	49903	SRR8883776	SRX5669577	SRS4612446	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		144 2 E08 KOcxcl12a 2	GSM3719004		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	144 2 E08 KOcxcl12a 2	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719004	GSM3719004: 144 2 E08 KOcxcl12a 2; Danio rerio; RNA Seq	GSM3719004		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719004	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			144-2-E08-KOcxcl12a-2_all_lanes_R1.fastq.gz 144-2-E08-KOcxcl12a-2_all_lanes_R2.fastq.gz	fastq fastq	109985812.0	742694.0	GSM3719004 r1	0:74.04 1:74.05	A:26580402;C:28348797;G:28922104;T:26031320;N:103189	74	74	26580402	28348797	28922104	26031320	103189	SRX5669577	SRS4612446	SRA798477	GEO	University of Oxford	2	0.93276	0.93175	0.25341	0.25219	0.78141	0.78405	0.65277	0.65585	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49904	49904	SRR8883775	SRX5669576	SRS4612445	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		143 2 E07 KOcxcl12a 1	GSM3719003		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	143 2 E07 KOcxcl12a 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719003	GSM3719003: 143 2 E07 KOcxcl12a 1; Danio rerio; RNA Seq	GSM3719003		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719003	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			143-2-E07-KOcxcl12a-1_all_lanes_R1.fastq.gz 143-2-E07-KOcxcl12a-1_all_lanes_R2.fastq.gz	fastq fastq	94811811.0	636658.0	GSM3719003 r1	0:74.46 1:74.46	A:22658972;C:24643435;G:25238963;T:22205729;N:64712	74	74	22658972	24643435	25238963	22205729	64712	SRX5669576	SRS4612445	SRA798477	GEO	University of Oxford	2	0.92745	0.92691	0.23249	0.23126	0.78658	0.79076	0.64976	0.63056	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49905	49905	SRR8883774	SRX5669575	SRS4612444	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		142 2 E06 KOcxcl12a ctr 3	GSM3719002		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	142 2 E06 KOcxcl12a ctr 3	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719002	GSM3719002: 142 2 E06 KOcxcl12a ctr 3; Danio rerio; RNA Seq	GSM3719002		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719002	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			142-2-E06-KOcxcl12a-ctr-3_all_lanes_R1.fastq.gz 142-2-E06-KOcxcl12a-ctr-3_all_lanes_R2.fastq.gz	fastq fastq	129809456.0	880087.0	GSM3719002 r1	0:73.75 1:73.75	A:30887867;C:33831790;G:34633569;T:30274300;N:181930	73	73	30887867	33831790	34633569	30274300	181930	SRX5669575	SRS4612444	SRA798477	GEO	University of Oxford	2	0.92838	0.92684	0.2376	0.23787	0.78636	0.79115	0.65598	0.63686	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49906	49906	SRR8883773	SRX5669574	SRS4612443	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		141 2 E05 KOcxcl12a ctr 2	GSM3719001		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	141 2 E05 KOcxcl12a ctr 2	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719001	GSM3719001: 141 2 E05 KOcxcl12a ctr 2; Danio rerio; RNA Seq	GSM3719001		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719001	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			141-2-E05-KOcxcl12a-ctr-2_all_lanes_R1.fastq.gz 141-2-E05-KOcxcl12a-ctr-2_all_lanes_R2.fastq.gz	fastq fastq	107380357.0	726760.0	GSM3719001 r1	0:73.87 1:73.88	A:26228066;C:27324290;G:27986915;T:25712036;N:129050	73	73	26228066	27324290	27986915	25712036	129050	SRX5669574	SRS4612443	SRA798477	GEO	University of Oxford	2	0.91412	0.91386	0.22813	0.22895	0.77784	0.78362	0.63341	0.63642	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49907	49907	SRR8883772	SRX5669573	SRS4612442	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		140 2 E04 KOcxcl12a ctr 1	GSM3719000		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	140 2 E04 KOcxcl12a ctr 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719000	GSM3719000: 140 2 E04 KOcxcl12a ctr 1; Danio rerio; RNA Seq	GSM3719000		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719000	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			140-2-E04-KOcxcl12a-ctr-1_all_lanes_R1.fastq.gz 140-2-E04-KOcxcl12a-ctr-1_all_lanes_R2.fastq.gz	fastq fastq	108418608.0	731612.0	GSM3719000 r1	0:74.10 1:74.09	A:26582166;C:27511188;G:28160622;T:26054265;N:110367	74	74	26582166	27511188	28160622	26054265	110367	SRX5669573	SRS4612442	SRA798477	GEO	University of Oxford	2	0.9189	0.91754	0.23947	0.23587	0.78084	0.78522	0.64092	0.59963	75	73	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49908	49908	SRR8883771	SRX5669572	SRS4612441	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		139 2 E03 KOtgm2b 6	GSM3718999		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	139 2 E03 KOtgm2b 6	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718999	GSM3718999: 139 2 E03 KOtgm2b 6; Danio rerio; RNA Seq	GSM3718999		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718999	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			139-2-E03-KOtgm2b-6_all_lanes_R1.fastq.gz 139-2-E03-KOtgm2b-6_all_lanes_R2.fastq.gz	fastq fastq	109962833.0	738854.0	GSM3718999 r1	0:74.41 1:74.42	A:26858777;C:28073839;G:28708123;T:26241362;N:80732	74	74	26858777	28073839	28708123	26241362	80732	SRX5669572	SRS4612441	SRA798477	GEO	University of Oxford	2	0.9353	0.93342	0.19619	0.19724	0.754	0.75607	0.60298	0.60929	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49909	49909	SRR8883770	SRX5669571	SRS4612440	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		138 2 E02 KOtgm2b 5	GSM3718998		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	138 2 E02 KOtgm2b 5	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718998	GSM3718998: 138 2 E02 KOtgm2b 5; Danio rerio; RNA Seq	GSM3718998		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718998	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			138-2-E02-KOtgm2b-5_all_lanes_R1.fastq.gz 138-2-E02-KOtgm2b-5_all_lanes_R2.fastq.gz	fastq fastq	100462360.0	671960.0	GSM3718998 r1	0:74.75 1:74.75	A:24544858;C:25599584;G:26221724;T:24054453;N:41741	74	74	24544858	25599584	26221724	24054453	41741	SRX5669571	SRS4612440	SRA798477	GEO	University of Oxford	2	0.94446	0.94375	0.19662	0.19723	0.75124	0.75588	0.58577	0.56794	76	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49910	49910	SRR8883769	SRX5669570	SRS4612439	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		137 2 E01 KOtgm2b 4	GSM3718997		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	137 2 E01 KOtgm2b 4	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718997	GSM3718997: 137 2 E01 KOtgm2b 4; Danio rerio; RNA Seq	GSM3718997		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718997	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			137-2-E01-KOtgm2b-4_all_lanes_R1.fastq.gz 137-2-E01-KOtgm2b-4_all_lanes_R2.fastq.gz	fastq fastq	106854841.0	717396.0	GSM3718997 r1	0:74.47 1:74.47	A:25509330;C:27879859;G:28531018;T:24874276;N:60358	74	74	25509330	27879859	28531018	24874276	60358	SRX5669570	SRS4612439	SRA798477	GEO	University of Oxford	2	0.92486	0.92304	0.21065	0.21002	0.77275	0.7777	0.63212	0.63504	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49911	49911	SRR8883768	SRX5669569	SRS4612438	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		136 2 D12 KOtgm2b 3	GSM3718996		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	136 2 D12 KOtgm2b 3	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718996	GSM3718996: 136 2 D12 KOtgm2b 3; Danio rerio; RNA Seq	GSM3718996		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718996	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			136-2-D12-KOtgm2b-3_all_lanes_R1.fastq.gz 136-2-D12-KOtgm2b-3_all_lanes_R2.fastq.gz	fastq fastq	92141370.0	620781.0	GSM3718996 r1	0:74.21 1:74.22	A:23141972;C:22908175;G:23441104;T:22555763;N:94356	74	74	23141972	22908175	23441104	22555763	94356	SRX5669569	SRS4612438	SRA798477	GEO	University of Oxford	2	0.92674	0.92438	0.19612	0.19794	0.74854	0.75755	0.55401	0.56341	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49912	49912	SRR8883767	SRX5669568	SRS4612437	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		135 2 D11 KOtgm2b 2	GSM3718995		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	135 2 D11 KOtgm2b 2	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718995	GSM3718995: 135 2 D11 KOtgm2b 2; Danio rerio; RNA Seq	GSM3718995		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718995	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			135-2-D11-KOtgm2b-2_all_lanes_R1.fastq.gz 135-2-D11-KOtgm2b-2_all_lanes_R2.fastq.gz	fastq fastq	66274479.0	443320.0	GSM3718995 r1	0:74.74 1:74.75	A:16243668;C:16886199;G:17301289;T:15810059;N:33264	74	74	16243668	16886199	17301289	15810059	33264	SRX5669568	SRS4612437	SRA798477	GEO	University of Oxford	2	0.93842	0.93704	0.22403	0.22571	0.7643	0.77218	0.62341	0.62445	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49913	49913	SRR8883766	SRX5669567	SRS4612436	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		134 2 D10 KOtgm2b 1	GSM3718994		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	134 2 D10 KOtgm2b 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718994	GSM3718994: 134 2 D10 KOtgm2b 1; Danio rerio; RNA Seq	GSM3718994		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718994	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			134-2-D10-KOtgm2b-1_all_lanes_R1.fastq.gz 134-2-D10-KOtgm2b-1_all_lanes_R2.fastq.gz	fastq fastq	60384203.0	405320.0	GSM3718994 r1	0:74.48 1:74.50	A:15095234;C:15063807;G:15456958;T:14724791;N:43413	74	74	15095234	15063807	15456958	14724791	43413	SRX5669567	SRS4612436	SRA798477	GEO	University of Oxford	2	0.92886	0.92692	0.21819	0.21631	0.7525	0.76077	0.53347	0.50585	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49914	49914	SRR8883765	SRX5669566	SRS4612435	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		133 2 D09 KOtgm2b ctr 3	GSM3718993		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	133 2 D09 KOtgm2b ctr 3	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718993	GSM3718993: 133 2 D09 KOtgm2b ctr 3; Danio rerio; RNA Seq	GSM3718993		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718993	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			133-2-D09-KOtgm2b-ctr-3_all_lanes_R1.fastq.gz 133-2-D09-KOtgm2b-ctr-3_all_lanes_R2.fastq.gz	fastq fastq	48591328.0	327743.0	GSM3718993 r1	0:74.13 1:74.13	A:12088250;C:12179083;G:12474240;T:11798218;N:51537	74	74	12088250	12179083	12474240	11798218	51537	SRX5669566	SRS4612435	SRA798477	GEO	University of Oxford	2	0.9338	0.93207	0.21936	0.22034	0.76359	0.76948	0.60676	0.59959	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49915	49915	SRR8883764	SRX5669565	SRS4612434	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		132 2 D08 KOtgm2b ctr 2	GSM3718992		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	132 2 D08 KOtgm2b ctr 2	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718992	GSM3718992: 132 2 D08 KOtgm2b ctr 2; Danio rerio; RNA Seq	GSM3718992		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718992	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			132-2-D08-KOtgm2b-ctr-2_all_lanes_R1.fastq.gz 132-2-D08-KOtgm2b-ctr-2_all_lanes_R2.fastq.gz	fastq fastq	49669187.0	334909.0	GSM3718992 r1	0:74.15 1:74.16	A:12028296;C:12782564;G:13085690;T:11722181;N:50456	74	74	12028296	12782564	13085690	11722181	50456	SRX5669565	SRS4612434	SRA798477	GEO	University of Oxford	2	0.93318	0.93238	0.21044	0.21218	0.76952	0.7783	0.62232	0.6203	76	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49916	49916	SRR8883763	SRX5669564	SRS4612433	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		131 2 D07 KOtgm2b ctr 1	GSM3718991		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	131 2 D07 KOtgm2b ctr 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718991	GSM3718991: 131 2 D07 KOtgm2b ctr 1; Danio rerio; RNA Seq	GSM3718991		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718991	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			131-2-D07-KOtgm2b-ctr-1_all_lanes_R1.fastq.gz 131-2-D07-KOtgm2b-ctr-1_all_lanes_R2.fastq.gz	fastq fastq	54297432.0	364230.0	GSM3718991 r1	0:74.54 1:74.54	A:13104680;C:14014488;G:14341190;T:12803752;N:33322	74	74	13104680	14014488	14341190	12803752	33322	SRX5669564	SRS4612433	SRA798477	GEO	University of Oxford	2	0.93946	0.94013	0.2414	0.23899	0.77674	0.78344	0.64098	0.61967	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49917	49917	SRR8883762	SRX5669563	SRS4612432	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		130 2 D06 KOsema3fb tbx18 1	GSM3718990		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	130 2 D06 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718990	GSM3718990: 130 2 D06 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718990		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718990	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			130-2-D06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 130-2-D06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	110234157.0	747392.0	GSM3718990 r1	0:73.74 1:73.76	A:28431221;C:26396031;G:27503562;T:27711266;N:192077	73	73	28431221	26396031	27503562	27711266	192077	SRX5669563	SRS4612432	SRA798477	GEO	University of Oxford	2	0.77713	0.76755	0.25874	0.25566	0.99117	0.99105	0.84401	0.71613	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49918	49918	SRR8883761	SRX5669562	SRS4612431	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		129 2 D05 KOsema3fb tbx18 1	GSM3718989		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	129 2 D05 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718989	GSM3718989: 129 2 D05 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718989		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718989	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			129-2-D05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 129-2-D05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	72776114.0	491364.0	GSM3718989 r1	0:74.05 1:74.06	A:18647181;C:17661907;G:18133434;T:18240577;N:93015	74	74	18647181	17661907	18133434	18240577	93015	SRX5669562	SRS4612431	SRA798477	GEO	University of Oxford	2	0.83344	0.82903	0.1213	0.12432	0.97388	0.9739	0.64406	0.65393	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49919	49919	SRR8883760	SRX5669561	SRS4612430	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		128 2 D04 KOsema3fb tbx18 1	GSM3718988		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	128 2 D04 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718988	GSM3718988: 128 2 D04 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718988		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718988	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			128-2-D04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 128-2-D04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	91788863.0	616504.0	GSM3718988 r1	0:74.44 1:74.45	A:25144004;C:20519360;G:21226945;T:24818679;N:79875	74	74	25144004	20519360	21226945	24818679	79875	SRX5669561	SRS4612430	SRA798477	GEO	University of Oxford	2	0.8087	0.80627	0.34661	0.34232	0.95763	0.95832	0.61953	0.64507	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49920	49920	SRR8883759	SRX5669560	SRS4612429	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		127 2 D03 KOsema3fb tbx18 1	GSM3718987		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	127 2 D03 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718987	GSM3718987: 127 2 D03 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718987		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718987	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			127-2-D03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 127-2-D03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	99060843.0	665407.0	GSM3718987 r1	0:74.43 1:74.44	A:26599641;C:22804504;G:23489807;T:26082542;N:84349	74	74	26599641	22804504	23489807	26082542	84349	SRX5669560	SRS4612429	SRA798477	GEO	University of Oxford	2	0.84494	0.84083	0.34251	0.3408	0.94846	0.94931	0.61735	0.62618	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49921	49921	SRR8883758	SRX5669559	SRS4612428	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		126 2 D02 KOsema3fb tbx18 1	GSM3718986		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	126 2 D02 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718986	GSM3718986: 126 2 D02 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718986		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718986	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			126-2-D02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 126-2-D02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	89497403.0	599998.0	GSM3718986 r1	0:74.58 1:74.58	A:23556468;C:21386062;G:21724809;T:22782097;N:47967	74	74	23556468	21386062	21724809	22782097	47967	SRX5669559	SRS4612428	SRA798477	GEO	University of Oxford	2	0.90048	0.90027	0.08906	0.09149	0.95136	0.95187	0.68687	0.69086	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49922	49922	SRR8883757	SRX5669558	SRS4612427	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		125 2 D01 KOsema3fb tbx18 1	GSM3718985		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	125 2 D01 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718985	GSM3718985: 125 2 D01 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718985		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718985	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			125-2-D01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 125-2-D01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	48185478.0	321734.0	GSM3718985 r1	0:74.88 1:74.89	A:12090976;C:12002728;G:12234353;T:11829653;N:27768	74	74	12090976	12002728	12234353	11829653	27768	SRX5669558	SRS4612427	SRA798477	GEO	University of Oxford	2	0.84457	0.84125	0.13895	0.13881	0.96625	0.96674	0.58767	0.58139	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49923	49923	SRR8883756	SRX5669557	SRS4612426	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		124 2 C12 KOsema3fb tbx18 1	GSM3718984		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	124 2 C12 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718984	GSM3718984: 124 2 C12 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718984		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718984	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			124-2-C12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 124-2-C12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	135607116.0	915406.0	GSM3718984 r1	0:74.07 1:74.07	A:32159235;C:34890150;G:36630005;T:31695707;N:232019	74	74	32159235	34890150	36630005	31695707	232019	SRX5669557	SRS4612426	SRA798477	GEO	University of Oxford	2	0.76677	0.75662	0.2656	0.26203	0.99492	0.99523	0.63635	0.65929	76	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49924	49924	SRR8883755	SRX5669556	SRS4612425	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		123 2 C11 KOsema3fb tbx18 1	GSM3718983		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	123 2 C11 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718983	GSM3718983: 123 2 C11 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718983		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718983	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			123-2-C11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 123-2-C11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	87497086.0	587638.0	GSM3718983 r1	0:74.45 1:74.45	A:23448862;C:20175987;G:21185040;T:22585978;N:101219	74	74	23448862	20175987	21185040	22585978	101219	SRX5669556	SRS4612425	SRA798477	GEO	University of Oxford	2	0.82255	0.81241	0.12138	0.12127	0.99711	0.99711	0.9386	0.93959	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49925	49925	SRR8883754	SRX5669555	SRS4612424	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		122 2 C10 KOsema3fb tbx18 1	GSM3718982		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	122 2 C10 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718982	GSM3718982: 122 2 C10 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718982		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718982	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			122-2-C10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 122-2-C10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	62517978.0	418828.0	GSM3718982 r1	0:74.64 1:74.63	A:16436794;C:14921072;G:15287825;T:15822124;N:50163	74	74	16436794	14921072	15287825	15822124	50163	SRX5669555	SRS4612424	SRA798477	GEO	University of Oxford	2	0.87516	0.87101	0.05328	0.05476	0.9514	0.95138	0.57772	0.62333	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49926	49926	SRR8883753	SRX5669554	SRS4612423	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		121 2 C09 KOsema3fb tbx18 1	GSM3718981		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	121 2 C09 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718981	GSM3718981: 121 2 C09 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718981		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718981	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			121-2-C09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 121-2-C09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	136153223.0	922773.0	GSM3718981 r1	0:73.77 1:73.77	A:37426170;C:30362404;G:31332794;T:36834225;N:197630	73	73	37426170	30362404	31332794	36834225	197630	SRX5669554	SRS4612423	SRA798477	GEO	University of Oxford	2	0.84938	0.84505	0.17896	0.18056	0.92427	0.92441	0.60599	0.59117	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49927	49927	SRR8883752	SRX5669553	SRS4612422	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		120 2 C08 KOsema3fb tbx18 1	GSM3718980		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	120 2 C08 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718980	GSM3718980: 120 2 C08 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718980		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718980	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			120-2-C08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 120-2-C08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	111876800.0	754706.0	GSM3718980 r1	0:74.12 1:74.12	A:29690879;C:25910779;G:26899072;T:29225413;N:150657	74	74	29690879	25910779	26899072	29225413	150657	SRX5669553	SRS4612422	SRA798477	GEO	University of Oxford	2	0.78833	0.78334	0.38511	0.382	0.96924	0.9694	0.68874	0.68759	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49928	49928	SRR8883744	SRX5669552	SRS4612421	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		119 2 C07 KOsema3fb tbx18 1	GSM3718979		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	119 2 C07 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718979	GSM3718979: 119 2 C07 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718979		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718979	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			119-2-C07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 119-2-C07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	156489712.0	1053300.0	GSM3718979 r1	0:74.29 1:74.28	A:45673694;C:32030116;G:33486582;T:45151963;N:147357	74	74	45673694	32030116	33486582	45151963	147357	SRX5669552	SRS4612421	SRA798477	GEO	University of Oxford	2	0.815	0.80967	0.35748	0.354	0.98031	0.98015	0.92183	0.91637	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49929	49929	SRR8883743	SRX5669551	SRS4612420	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		118 2 C06 KOsema3fb tbx18 1	GSM3718978		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	118 2 C06 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718978	GSM3718978: 118 2 C06 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718978		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718978	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			118-2-C06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 118-2-C06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	97946060.0	657322.0	GSM3718978 r1	0:74.50 1:74.51	A:28975729;C:19954414;G:20745385;T:28174552;N:95980	74	74	28975729	19954414	20745385	28174552	95980	SRX5669551	SRS4612420	SRA798477	GEO	University of Oxford	2	0.88899	0.88117	0.01232	0.01239	0.99823	0.99825	0.82129	0.81747	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49930	49930	SRR8883742	SRX5669550	SRS4612419	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		117 2 C05 KOsema3fb tbx18 1	GSM3718977		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	117 2 C05 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718977	GSM3718977: 117 2 C05 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718977		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718977	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			117-2-C05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 117-2-C05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	69214846.0	465753.0	GSM3718977 r1	0:74.30 1:74.31	A:18761059;C:15617433;G:16216548;T:18532653;N:87153	74	74	18761059	15617433	16216548	18532653	87153	SRX5669550	SRS4612419	SRA798477	GEO	University of Oxford	2	0.76854	0.76093	0.15615	0.15563	0.93066	0.93119	0.58239	0.60187	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49931	49931	SRR8883741	SRX5669549	SRS4612418	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		116 2 C04 KOsema3fb tbx18 1	GSM3718976		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	116 2 C04 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718976	GSM3718976: 116 2 C04 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718976		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718976	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			116-2-C04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 116-2-C04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	75472427.0	507600.0	GSM3718976 r1	0:74.34 1:74.34	A:20859539;C:16681986;G:17258567;T:20586679;N:85656	74	74	20859539	16681986	17258567	20586679	85656	SRX5669549	SRS4612418	SRA798477	GEO	University of Oxford	2	0.81342	0.80704	0.26123	0.25994	0.9347	0.93464	0.54291	0.54243	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49932	49932	SRR8883740	SRX5669548	SRS4612417	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		115 2 C03 KOsema3fb tbx18 1	GSM3718975		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	115 2 C03 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718975	GSM3718975: 115 2 C03 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718975		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718975	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			115-2-C03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 115-2-C03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	82962806.0	556564.0	GSM3718975 r1	0:74.53 1:74.53	A:23001088;C:18396897;G:18830206;T:22674040;N:60575	74	74	23001088	18396897	18830206	22674040	60575	SRX5669548	SRS4612417	SRA798477	GEO	University of Oxford	2	0.89917	0.89649	0.161	0.16093	0.92443	0.92468	0.59905	0.60072	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49933	49933	SRR8883739	SRX5669547	SRS4612416	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		114 2 C02 KOsema3fb tbx18 1	GSM3718974		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	114 2 C02 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718974	GSM3718974: 114 2 C02 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718974		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718974	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			114-2-C02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 114-2-C02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	106216907.0	712267.0	GSM3718974 r1	0:74.56 1:74.56	A:29174324;C:23794193;G:24434136;T:28754518;N:59736	74	74	29174324	23794193	24434136	28754518	59736	SRX5669547	SRS4612416	SRA798477	GEO	University of Oxford	2	0.90487	0.90038	0.29101	0.29055	0.88176	0.88258	0.55682	0.55632	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49934	49934	SRR8883738	SRX5669546	SRS4612415	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		113 2 C01 KOsema3fb tbx18 1	GSM3718973		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	113 2 C01 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718973	GSM3718973: 113 2 C01 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718973		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718973	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			113-2-C01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 113-2-C01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	131443192.0	885217.0	GSM3718973 r1	0:74.24 1:74.24	A:33392659;C:31910928;G:33134031;T:32853539;N:152035	74	74	33392659	31910928	33134031	32853539	152035	SRX5669546	SRS4612415	SRA798477	GEO	University of Oxford	2	0.76875	0.763	0.34113	0.33651	0.98236	0.98238	0.7352	0.71836	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49935	49935	SRR8883737	SRX5669545	SRS4612414	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		112 2 B12 KOsema3fb tbx18 1	GSM3718972		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	112 2 B12 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718972	GSM3718972: 112 2 B12 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718972		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718972	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			112-2-B12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 112-2-B12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	75374963.0	504536.0	GSM3718972 r1	0:74.69 1:74.70	A:19871639;C:17630596;G:18334709;T:19474458;N:63561	74	74	19871639	17630596	18334709	19474458	63561	SRX5669545	SRS4612414	SRA798477	GEO	University of Oxford	2	0.79501	0.78698	0.31679	0.31493	0.97126	0.97161	0.69061	0.68695	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49936	49936	SRR8883736	SRX5669544	SRS4612413	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		111 2 B11 KOsema3fb tbx18 1	GSM3718971		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	111 2 B11 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718971	GSM3718971: 111 2 B11 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718971		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718971	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			111-2-B11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 111-2-B11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	61306141.0	409447.0	GSM3718971 r1	0:74.86 1:74.87	A:17078666;C:13397099;G:14017031;T:16767954;N:45391	74	74	17078666	13397099	14017031	16767954	45391	SRX5669544	SRS4612413	SRA798477	GEO	University of Oxford	2	0.78279	0.77063	0.29509	0.2912	0.94943	0.94972	0.68066	0.66888	76	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49937	49937	SRR8883735	SRX5669543	SRS4612412	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		110 2 B09 KOsema3fb tbx18 1	GSM3718970		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	110 2 B09 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718970	GSM3718970: 110 2 B09 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718970		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			110-2-B09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 110-2-B09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	77611492.0	517973.0	GSM3718970 r1	0:74.92 1:74.92	A:20828796;C:18000975;G:18473556;T:20273490;N:34675	74	74	20828796	18000975	18473556	20273490	34675	SRX5669543	SRS4612412	SRA798477	GEO	University of Oxford	2	0.8943	0.8898	0.07119	0.07297	0.96376	0.96376	0.65962	0.66776	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49938	49938	SRR8883734	SRX5669542	SRS4612411	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		109 2 B08 KOsema3fb tbx18 1	GSM3718969		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	109 2 B08 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718969	GSM3718969: 109 2 B08 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718969		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718969	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			109-2-B08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 109-2-B08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	129418006.0	863669.0	GSM3718969 r1	0:74.92 1:74.92	A:38739420;C:25964234;G:27042729;T:37614526;N:57097	74	74	38739420	25964234	27042729	37614526	57097	SRX5669542	SRS4612411	SRA798477	GEO	University of Oxford	2	0.90082	0.89259	0.10991	0.10917	0.99383	0.99371	0.98678	0.98259	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49939	49939	SRR8883733	SRX5669541	SRS4612410	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		108 2 B07 KOsema3fb tbx18 1	GSM3718968		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	108 2 B07 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718968	GSM3718968: 108 2 B07 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718968		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718968	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			108-2-B07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 108-2-B07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	64293554.0	427843.0	GSM3718968 r1	0:75.14 1:75.14	A:16371370;C:15659136;G:16037461;T:16204914;N:20673	75	75	16371370	15659136	16037461	16204914	20673	SRX5669541	SRS4612410	SRA798477	GEO	University of Oxford	2	0.88538	0.88147	0.09713	0.10128	0.96408	0.96414	0.57841	0.57128	74	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49940	49940	SRR8883732	SRX5669540	SRS4612409	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		107 2 B06 KOsema3fb tbx18 1	GSM3718967		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	107 2 B06 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718967	GSM3718967: 107 2 B06 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718967		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718967	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			107-2-B06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 107-2-B06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	87019759.0	578810.0	GSM3718967 r1	0:75.17 1:75.17	A:24569329;C:18725958;G:19314464;T:24386952;N:23056	75	75	24569329	18725958	19314464	24386952	23056	SRX5669540	SRS4612409	SRA798477	GEO	University of Oxford	2	0.88053	0.87769	0.22651	0.22723	0.93103	0.93178	0.6335	0.54178	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49941	49941	SRR8883731	SRX5669539	SRS4612408	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		106 2 B05 KOsema3fb tbx18 1	GSM3718966		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	106 2 B05 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718966	GSM3718966: 106 2 B05 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718966		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718966	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			106-2-B05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 106-2-B05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	171458105.0	1143747.0	GSM3718966 r1	0:74.95 1:74.96	A:46877212;C:38285761;G:39836533;T:46388650;N:69949	74	74	46877212	38285761	39836533	46388650	69949	SRX5669539	SRS4612408	SRA798477	GEO	University of Oxford	2	0.8191	0.81279	0.43731	0.43052	0.98397	0.98533	0.83233	0.63073	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49942	49942	SRR8883730	SRX5669538	SRS4612407	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		105 2 B04 KOsema3fb tbx18 1	GSM3718965		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	105 2 B04 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718965	GSM3718965: 105 2 B04 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718965		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718965	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			105-2-B04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 105-2-B04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	127662981.0	854443.0	GSM3718965 r1	0:74.70 1:74.71	A:29584063;C:34031538;G:35345753;T:28597787;N:103840	74	74	29584063	34031538	35345753	28597787	103840	SRX5669538	SRS4612407	SRA798477	GEO	University of Oxford	2	0.68467	0.67957	0.25187	0.2499	0.99502	0.99502	0.7152	0.71768	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49943	49943	SRR8883729	SRX5669537	SRS4612406	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		104 2 B03 KOsema3fb tbx18 1	GSM3718964		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	104 2 B03 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718964	GSM3718964: 104 2 B03 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718964		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718964	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			104-2-B03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 104-2-B03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	115513857.0	770881.0	GSM3718964 r1	0:74.92 1:74.92	A:31108404;C:26544217;G:27186178;T:30628629;N:46429	74	74	31108404	26544217	27186178	30628629	46429	SRX5669537	SRS4612406	SRA798477	GEO	University of Oxford	2	0.88682	0.88375	0.21439	0.21595	0.93787	0.93736	0.51052	0.51032	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49944	49944	SRR8883728	SRX5669536	SRS4612405	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		103 2 B02 KOsema3fb tbx18 1	GSM3718963		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	103 2 B02 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718963	GSM3718963: 103 2 B02 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718963		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718963	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			103-2-B02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 103-2-B02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	192832844.0	1295164.0	GSM3718963 r1	0:74.44 1:74.44	A:52098091;C:43785153;G:45595134;T:51197425;N:157041	74	74	52098091	43785153	45595134	51197425	157041	SRX5669536	SRS4612405	SRA798477	GEO	University of Oxford	2	0.81383	0.80831	0.24437	0.24477	0.95586	0.95668	0.78895	0.7856	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49945	49945	SRR8883727	SRX5669535	SRS4612404	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		102 2 B01 KOsema3fb tbx18 1	GSM3718962		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	102 2 B01 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718962	GSM3718962: 102 2 B01 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718962		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718962	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			102-2-B01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 102-2-B01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	120333848.0	804439.0	GSM3718962 r1	0:74.79 1:74.79	A:32682684;C:27190840;G:28132999;T:32250173;N:77152	74	74	32682684	27190840	28132999	32250173	77152	SRX5669535	SRS4612404	SRA798477	GEO	University of Oxford	2	0.83759	0.83074	0.21978	0.21999	0.936	0.93647	0.56733	0.56679	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49946	49946	SRR8883726	SRX5669534	SRS4612403	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		101 2 A12 KOsema3fb tbx18 1	GSM3718961		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	101 2 A12 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718961	GSM3718961: 101 2 A12 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718961		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718961	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			101-2-A12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 101-2-A12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	65436843.0	438922.0	GSM3718961 r1	0:74.54 1:74.54	A:17612386;C:14944988;G:15465948;T:17344793;N:68728	74	74	17612386	14944988	15465948	17344793	68728	SRX5669534	SRS4612403	SRA798477	GEO	University of Oxford	2	0.85881	0.85199	0.28877	0.28733	0.95826	0.95893	0.76754	0.62031	71	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49947	49947	SRR8883725	SRX5669533	SRS4612402	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		100 2 A11 KOsema3fb tbx18 1	GSM3718960		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	100 2 A11 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718960	GSM3718960: 100 2 A11 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718960		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718960	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			100-2-A11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 100-2-A11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	140310657.0	949434.0	GSM3718960 r1	0:73.89 1:73.89	A:42097554;C:28046328;G:29209965;T:40762460;N:194350	73	73	42097554	28046328	29209965	40762460	194350	SRX5669533	SRS4612402	SRA798477	GEO	University of Oxford	2	0.87505	0.86715	0.0038	0.00397	0.99845	0.99866	0.9972	0.97282	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49948	49948	SRR8883724	SRX5669532	SRS4612401	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		099 2 A10 KOsema3fb tbx18 1	GSM3718959		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	099 2 A10 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718959	GSM3718959: 099 2 A10 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718959		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718959	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			099-2-A10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 099-2-A10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	132323171.0	896345.0	GSM3718959 r1	0:73.81 1:73.81	A:35858895;C:29635963;G:31229716;T:35354644;N:243953	73	73	35858895	29635963	31229716	35354644	243953	SRX5669532	SRS4612401	SRA798477	GEO	University of Oxford	2	0.77424	0.76268	0.22514	0.2202	0.98652	0.98695	0.86437	0.87792	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49949	49949	SRR8883723	SRX5669531	SRS4612400	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		098 2 A09 KOsema3fb tbx18 1	GSM3718958		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	098 2 A09 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718958	GSM3718958: 098 2 A09 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718958		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718958	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			098-2-A09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 098-2-A09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	114456948.0	771559.0	GSM3718958 r1	0:74.17 1:74.17	A:31737943;C:25279629;G:26036188;T:31288498;N:114690	74	74	31737943	25279629	26036188	31288498	114690	SRX5669531	SRS4612400	SRA798477	GEO	University of Oxford	2	0.87167	0.86804	0.23167	0.23179	0.92011	0.92062	0.53072	0.5313	74	74	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49950	49950	SRR8883722	SRX5669530	SRS4612399	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		097 2 A08 KOsema3fb tbx18 1	GSM3718957		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	097 2 A08 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718957	GSM3718957: 097 2 A08 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718957		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718957	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			097-2-A08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 097-2-A08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	73333087.0	494843.0	GSM3718957 r1	0:74.08 1:74.11	A:20100557;C:16284330;G:17212076;T:19600158;N:135966	74	74	20100557	16284330	17212076	19600158	135966	SRX5669530	SRS4612399	SRA798477	GEO	University of Oxford	2	0.58813	0.57236	0.34093	0.32937	0.98839	0.98851	0.779	0.72827	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49951	49951	SRR8883721	SRX5669529	SRS4612398	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		096 2 A06 KOsema3fb tbx18 1	GSM3718956		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	096 2 A06 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718956	GSM3718956: 096 2 A06 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718956		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718956	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			096-2-A06-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 096-2-A06-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	90842172.0	611862.0	GSM3718956 r1	0:74.23 1:74.24	A:23965966;C:21373491;G:21862424;T:23547639;N:92652	74	74	23965966	21373491	21862424	23547639	92652	SRX5669529	SRS4612398	SRA798477	GEO	University of Oxford	2	0.8843	0.88141	0.07106	0.07335	0.95152	0.95134	0.66617	0.66026	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49952	49952	SRR8883720	SRX5669528	SRS4612397	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		095 2 A05 KOsema3fb tbx18 1	GSM3718955		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	095 2 A05 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718955	GSM3718955: 095 2 A05 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718955		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718955	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			095-2-A05-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 095-2-A05-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	77815127.0	524581.0	GSM3718955 r1	0:74.18 1:74.16	A:21934006;C:16958511;G:17457568;T:21408772;N:56270	74	74	21934006	16958511	17457568	21408772	56270	SRX5669528	SRS4612397	SRA798477	GEO	University of Oxford	2	0.91045	0.90324	0.15048	0.14704	0.90611	0.90778	0.61827	0.61537	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49953	49953	SRR8883719	SRX5669527	SRS4612396	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		094 2 A04 KOsema3fb tbx18 1	GSM3718954		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	094 2 A04 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718954	GSM3718954: 094 2 A04 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718954		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718954	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			094-2-A04-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 094-2-A04-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	150930160.0	1017672.0	GSM3718954 r1	0:74.15 1:74.16	A:46095353;C:29229977;G:30487780;T:44969159;N:147891	74	74	46095353	29229977	30487780	44969159	147891	SRX5669527	SRS4612396	SRA798477	GEO	University of Oxford	2	0.89968	0.89516	0.15644	0.15583	0.98965	0.98957	0.90884	0.88342	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49954	49954	SRR8883718	SRX5669526	SRS4612395	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		093 2 A03 KOsema3fb tbx18 1	GSM3718953		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	093 2 A03 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718953	GSM3718953: 093 2 A03 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718953		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718953	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			093-2-A03-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 093-2-A03-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	144217761.0	973753.0	GSM3718953 r1	0:74.05 1:74.06	A:39154057;C:32680762;G:33686996;T:38528147;N:167799	74	74	39154057	32680762	33686996	38528147	167799	SRX5669526	SRS4612395	SRA798477	GEO	University of Oxford	2	0.85323	0.8494	0.3006	0.30141	0.94655	0.94679	0.58374	0.59101	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49955	49955	SRR8883717	SRX5669525	SRS4612394	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		092 2 A02 KOsema3fb tbx18 1	GSM3718952		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	092 2 A02 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718952	GSM3718952: 092 2 A02 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718952		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718952	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			092-2-A02-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 092-2-A02-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	124615116.0	836655.0	GSM3718952 r1	0:74.47 1:74.47	A:29165184;C:32964210;G:34113962;T:28256712;N:115048	74	74	29165184	32964210	34113962	28256712	115048	SRX5669525	SRS4612394	SRA798477	GEO	University of Oxford	2	0.80508	0.80178	0.26378	0.26378	0.99141	0.99133	0.707	0.65919	73	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49956	49956	SRR8883716	SRX5669524	SRS4612393	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		091 2 A01 KOsema3fb tbx18 1	GSM3718951		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	091 2 A01 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718951	GSM3718951: 091 2 A01 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718951		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718951	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			091-2-A01-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 091-2-A01-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	130111864.0	870690.0	GSM3718951 r1	0:74.72 1:74.72	A:37160441;C:27653019;G:28922504;T:36294701;N:81199	74	74	37160441	27653019	28922504	36294701	81199	SRX5669524	SRS4612393	SRA798477	GEO	University of Oxford	2	0.8646	0.85823	0.13494	0.13789	0.9934	0.9933	0.94953	0.94841	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49957	49957	SRR8883715	SRX5669523	SRS4612392	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		090 1 H12 KOsema3fb tbx18 1	GSM3718950		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	090 1 H12 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718950	GSM3718950: 090 1 H12 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718950		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718950	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			090-1-H12-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 090-1-H12-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	149578485.0	1002183.0	GSM3718950 r1	0:74.63 1:74.62	A:38597080;C:36561279;G:37234713;T:37123758;N:61655	74	74	38597080	36561279	37234713	37123758	61655	SRX5669523	SRS4612392	SRA798477	GEO	University of Oxford	2	0.91419	0.91521	0.10566	0.10682	0.93143	0.93133	0.63762	0.63312	76	75	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49958	49958	SRR8883714	SRX5669522	SRS4612391	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		089 1 H11 KOsema3fb tbx18 1	GSM3718949		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	089 1 H11 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718949	GSM3718949: 089 1 H11 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718949		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718949	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			089-1-H11-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz 089-1-H11-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz	fastq fastq	181404476.0	1216282.0	GSM3718949 r1	0:74.57 1:74.57	A:43064417;C:47397029;G:49107412;T:41710650;N:124968	74	74	43064417	47397029	49107412	41710650	124968	SRX5669522	SRS4612391	SRA798477	GEO	University of Oxford	2	0.77119	0.76546	0.25328	0.25162	0.99371	0.99375	0.7712	0.79784	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49959	49959	SRR8883713	SRX5669521	SRS4612390	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		088 1 H10 KOsema3fb tbx18 1	GSM3718948		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	088 1 H10 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718948	GSM3718948: 088 1 H10 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718948		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718948	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			088-1-H10-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 088-1-H10-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	141673238.0	952834.0	GSM3718948 r1	0:74.34 1:74.34	A:34350000;C:36603083;G:37520883;T:33109631;N:89641	74	74	34350000	36603083	37520883	33109631	89641	SRX5669521	SRS4612390	SRA798477	GEO	University of Oxford	2	0.79667	0.79244	0.28634	0.28347	0.96366	0.96321	0.6333	0.68112	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49960	49960	SRR8883712	SRX5669520	SRS4612389	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		087 1 H09 KOsema3fb tbx18 1	GSM3718947		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	087 1 H09 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718947	GSM3718947: 087 1 H09 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718947		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718947	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			087-1-H09-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 087-1-H09-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	156833870.0	1059269.0	GSM3718947 r1	0:74.04 1:74.02	A:39115526;C:39464692;G:40259183;T:37861574;N:132895	74	74	39115526	39464692	40259183	37861574	132895	SRX5669520	SRS4612389	SRA798477	GEO	University of Oxford	2	0.83542	0.83393	0.10395	0.10686	0.97532	0.9753	0.6127	0.61353	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49961	49961	SRR8883711	SRX5669519	SRS4612388	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		086 1 H08 KOsema3fb tbx18 1	GSM3718946		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	086 1 H08 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718946	GSM3718946: 086 1 H08 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718946		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718946	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			086-1-H08-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 086-1-H08-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	141486517.0	946739.0	GSM3718946 r1	0:74.73 1:74.72	A:34720035;C:36172265;G:36926372;T:33608900;N:58945	74	74	34720035	36172265	36926372	33608900	58945	SRX5669519	SRS4612388	SRA798477	GEO	University of Oxford	2	0.85483	0.854	0.13126	0.13493	0.96917	0.96938	0.56895	0.57342	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49962	49962	SRR8883710	SRX5669518	SRS4612387	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		085 1 H07 KOsema3fb tbx18 1	GSM3718945		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	085 1 H07 KOsema3fb tbx18 1	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718945	GSM3718945: 085 1 H07 KOsema3fb tbx18 1; Danio rerio; RNA Seq	GSM3718945		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718945	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			085-1-H07-KOsema3fb-tbx18-1_all_lanes_R1.fastq.gz 085-1-H07-KOsema3fb-tbx18-1_all_lanes_R2.fastq.gz	fastq fastq	160038205.0	1074199.0	GSM3718945 r1	0:74.49 1:74.49	A:42350221;C:37069067;G:38413049;T:42051865;N:154003	74	74	42350221	37069067	38413049	42051865	154003	SRX5669518	SRS4612387	SRA798477	GEO	University of Oxford	2	0.73986	0.73837	0.33609	0.33447	0.97619	0.97615	0.73697	0.72259	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;