metadata: run_metadata: 499 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and technology = "generic-scrnaseq-only"

499 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and technology = "generic-scrnaseq-only"

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.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
19476	19476	ERR14208827	ERX13611047	ERS22979745	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 1 sample	SAMEA117628607	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 004\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 004\|scientific name:Danio rerio									Raw reads: Scrambled 1 sample	webin reads Scrambled 1 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F04.bam	bam	8497741.0	104283.0	webin reads Scrambled 1 sample	0:81.49	A:2628864;C:1112827;G:2146146;T:2609768;N:136	81		2628864	1112827	2146146	2609768	136	ERX13611047	ERS22979745	ERA31123309	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19477	19477	ERR14208813	ERX13611033	ERS22979748	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 1 sample	SAMEA117628610	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 007\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 007\|scientific name:Danio rerio									Raw reads: ythdf2KO 1 sample	webin reads ythdf2KO 1 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D09.bam	bam	673213184.0	8122011.0	webin reads ythdf2KO 1 sample	0:82.89	A:180836688;C:107076381;G:193711319;T:191586188;N:2608	82		180836688	107076381	193711319	191586188	2608	ERX13611033	ERS22979748	ERA31123295	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19478	19478	ERR14208811	ERX13611031	ERS22979755	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 6 sample	SAMEA117628617	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 014\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 014\|scientific name:Danio rerio									Raw reads: GFP 6 sample	webin reads GFP 6 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 6 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	H01.bam	bam	337553787.0	3153658.0	webin reads GFP 6 sample	0:107.04	A:81816649;C:55524538;G:113686171;T:86525390;N:1039	107		81816649	55524538	113686171	86525390	1039	ERX13611031	ERS22979755	ERA31123293	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19479	19479	ERR14208821	ERX13611041	ERS22979752	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 5 sample	SAMEA117628614	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 011\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 011\|scientific name:Danio rerio									Raw reads: ythdf2KO 5 sample	webin reads ythdf2KO 5 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G10.bam	bam	226771232.0	2050630.0	webin reads ythdf2KO 5 sample	0:110.59	A:56944731;C:30766256;G:83820146;T:55239221;N:878	110		56944731	30766256	83820146	55239221	878	ERX13611041	ERS22979752	ERA31123303	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19480	19480	ERR14208818	ERX13611038	ERS22979750	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 3 sample	SAMEA117628612	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 009\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 009\|scientific name:Danio rerio									Raw reads: ythdf2KO 3 sample	webin reads ythdf2KO 3 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G08.bam	bam	351425328.0	3771763.0	webin reads ythdf2KO 3 sample	0:93.17	A:83933175;C:50138103;G:128300798;T:89051913;N:1339	93		83933175	50138103	128300798	89051913	1339	ERX13611038	ERS22979750	ERA31123300	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19481	19481	ERR14208826	ERX13611046	ERS22979758	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 3 sample	SAMEA117628620	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 017\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 017\|scientific name:Danio rerio									Raw reads: YTHDF2 3 sample	webin reads YTHDF2 3 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	E01.bam	bam	181017083.0	1670383.0	webin reads YTHDF2 3 sample	0:108.37	A:38910474;C:31607688;G:67095095;T:43403227;N:599	108		38910474	31607688	67095095	43403227	599	ERX13611046	ERS22979758	ERA31123308	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19482	19482	ERR14208815	ERX13611035	ERS22979749	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 2 sample	SAMEA117628611	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 008\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 008\|scientific name:Danio rerio									Raw reads: ythdf2KO 2 sample	webin reads ythdf2KO 2 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D10.bam	bam	282414832.0	2675188.0	webin reads ythdf2KO 2 sample	0:105.57	A:73651155;C:41694223;G:96485766;T:70582706;N:982	105		73651155	41694223	96485766	70582706	982	ERX13611035	ERS22979749	ERA31123297	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19483	19483	ERR14208804	ERX13611024	ERS22979742	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 1 sample	SAMEA117628604	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 001\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 001\|scientific name:Danio rerio									Raw reads: GFP 1 sample	webin reads GFP 1 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F01.bam	bam	8036009.0	97716.0	webin reads GFP 1 sample	0:82.24	A:2445867;C:1074319;G:2086526;T:2429153;N:144	82		2445867	1074319	2086526	2429153	144	ERX13611024	ERS22979742	ERA31123286	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19484	19484	ERR14208829	ERX13611049	ERS22979747	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 3 sample	SAMEA117628609	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 006\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 006\|scientific name:Danio rerio									Raw reads: Scrambled 3 sample	webin reads Scrambled 3 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F06.bam	bam	90051514.0	910768.0	webin reads Scrambled 3 sample	0:98.87	A:30132090;C:13700682;G:16323331;T:29894332;N:1079	98		30132090	13700682	16323331	29894332	1079	ERX13611049	ERS22979747	ERA31123311	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19485	19485	ERR14208809	ERX13611029	ERS22979753	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 4 sample	SAMEA117628615	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 012\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 012\|scientific name:Danio rerio									Raw reads: GFP 4 sample	webin reads GFP 4 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G11.bam	bam	72278736.0	751207.0	webin reads GFP 4 sample	0:96.22	A:17589630;C:11153310;G:25212154;T:18323416;N:226	96		17589630	11153310	25212154	18323416	226	ERX13611029	ERS22979753	ERA31123291	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19486	19486	ERR14208806	ERX13611026	ERS22979743	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 2 sample	SAMEA117628605	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 002\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 002\|scientific name:Danio rerio									Raw reads: GFP 2 sample	webin reads GFP 2 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F02.bam	bam	19196592.0	230075.0	webin reads GFP 2 sample	0:83.44	A:5957309;C:2709511;G:4434875;T:6094552;N:345	83		5957309	2709511	4434875	6094552	345	ERX13611026	ERS22979743	ERA31123288	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19487	19487	ERR14208810	ERX13611030	ERS22979754	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 5 sample	SAMEA117628616	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 013\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 013\|scientific name:Danio rerio									Raw reads: GFP 5 sample	webin reads GFP 5 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 5 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G12.bam	bam	431708790.0	5173015.0	webin reads GFP 5 sample	0:83.45	A:119077902;C:68329173;G:126879243;T:117420803;N:1669	83		119077902	68329173	126879243	117420803	1669	ERX13611030	ERS22979754	ERA31123292	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19488	19488	ERR14208828	ERX13611048	ERS22979746	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	Scrambled 2 sample	SAMEA117628608	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 005\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 005\|scientific name:Danio rerio									Raw reads: Scrambled 2 sample	webin reads Scrambled 2 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: Scrambled 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F05.bam	bam	32695808.0	357320.0	webin reads Scrambled 2 sample	0:91.50	A:10989624;C:4719485;G:5954777;T:11031603;N:319	91		10989624	4719485	5954777	11031603	319	ERX13611048	ERS22979746	ERA31123310	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19489	19489	ERR14208819	ERX13611039	ERS22979751	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	ythdf2KO 4 sample	SAMEA117628613	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 010\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 010\|scientific name:Danio rerio									Raw reads: ythdf2KO 4 sample	webin reads ythdf2KO 4 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: ythdf2KO 4 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	G09.bam	bam	254231539.0	2766205.0	webin reads ythdf2KO 4 sample	0:91.91	A:63984512;C:40328422;G:86431821;T:63485754;N:1030	91		63984512	40328422	86431821	63485754	1030	ERX13611039	ERS22979751	ERA31123301	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19490	19490	ERR14208808	ERX13611028	ERS22979744	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	GFP 3 sample	SAMEA117628606	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 003\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 003\|scientific name:Danio rerio									Raw reads: GFP 3 sample	webin reads GFP 3 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: GFP 3 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	F03.bam	bam	35932988.0	419944.0	webin reads GFP 3 sample	0:85.57	A:11252929;C:5321445;G:8032297;T:11325814;N:503	85		11252929	5321445	8032297	11325814	503	ERX13611028	ERS22979744	ERA31123290	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19491	19491	ERR14208825	ERX13611045	ERS22979757	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 2 sample	SAMEA117628619	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 016\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 016\|scientific name:Danio rerio									Raw reads: YTHDF2 2 sample	webin reads YTHDF2 2 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 2 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D12.bam	bam	626993184.0	7599502.0	webin reads YTHDF2 2 sample	0:82.50	A:182701108;C:91008174;G:172822143;T:180459253;N:2506	82		182701108	91008174	172822143	180459253	2506	ERX13611045	ERS22979757	ERA31123307	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
19492	19492	ERR14208822	ERX13611042	ERS22979756	ERP167299	PRJEB83709	YTHDF2 and ASD DM	3296f78e-e1c0-43ea-968c-53fe04e67615	Other	Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01		Single cell RNA sequencing of zebrafish heads	YTHDF2 1 sample	SAMEA117628618	UNIVERSITY OF CALIFORNIA - DAVIS	ENA first public:2025 02 01\|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS\|INSDC status:public\|Submitter Id:Sample 015\|collection date:2022 08 07\|common name:zebrafish\|dev stage:72 hpf\|geographic location country and/or sea:USA\|sample name:Sample 015\|scientific name:Danio rerio									Raw reads: YTHDF2 1 sample	webin reads YTHDF2 1 sample	unspecified			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	ERP167299	Raw reads: YTHDF2 1 sample	ENA FIRST PUBLIC:2025 02 01\|ENA LAST UPDATE:2025 02 01	D11.bam	bam	120748751.0	1368887.0	webin reads YTHDF2 1 sample	0:88.21	A:34957526;C:19985010;G:32927086;T:32878659;N:470	88		34957526	19985010	32927086	32878659	470	ERX13611042	ERS22979756	ERA31123304	UNIVERSITY OF CALIFORNIA - DAVIS\|European Nucleotide Archive	UNIVERSITY OF CALIFORNIA - DAVIS							B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_generic	generic-scrnaseq-only	United States	2025-02-01	Larval	Larval	Head	Nervous System
41355	41355	SRR4342171	SRX2209226	SRS1726586	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 9pos	GSM2334964		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:9	tbx5 9pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:9	GSM2334964	GSM2334964: tbx5 9pos; Danio rerio; RNA Seq	GSM2334964	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334964	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_9pos__HectorSanchez_RNA_Seq_OvationSC_ACCTCA_L002_R1_001.fastq.gz	fastq	783131298.0	12838218.0	GSM2334964 r1	0:61	A:231794213;C:152686156;G:196289761;T:202337851;N:23317	61		231794213	152686156	196289761	202337851	23317	SRX2209226	SRS1726586	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.91274	0.14772	0.85084	0.58033	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41356	41356	SRR4342170	SRX2209225	SRS1726587	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 9neg	GSM2334963		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:9	tbx5 9neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:9	GSM2334963	GSM2334963: tbx5 9neg; Danio rerio; RNA Seq	GSM2334963	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334963	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_9neg__HectorSanchez_RNA_Seq_OvationSC_GTGCTT_L002_R1_001.fastq.gz	fastq	597229833.0	9790653.0	GSM2334963 r1	0:61	A:182072130;C:116058906;G:143260521;T:155820528;N:17748	61		182072130	116058906	143260521	155820528	17748	SRX2209225	SRS1726587	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.8964	0.14551	0.85612	0.54858	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41357	41357	SRR4342169	SRX2209224	SRS1726585	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 8pos	GSM2334962		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:8	tbx5 8pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:8	GSM2334962	GSM2334962: tbx5 8pos; Danio rerio; RNA Seq	GSM2334962	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334962	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_8pos__HectorSanchez_RNA_Seq_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	749298746.0	12283586.0	GSM2334962 r1	0:61	A:223933431;C:143222641;G:189173448;T:192959794;N:9432	61		223933431	143222641	189173448	192959794	9432	SRX2209224	SRS1726585	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.91034	0.13718	0.85192	0.56656	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41358	41358	SRR4342168	SRX2209223	SRS1726584	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 8neg	GSM2334961		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:8	tbx5 8neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:8	GSM2334961	GSM2334961: tbx5 8neg; Danio rerio; RNA Seq	GSM2334961	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334961	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_8neg__HectorSanchez_RNA_Seq_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	671219417.0	11003597.0	GSM2334961 r1	0:61	A:200873049;C:127618001;G:167285388;T:175434453;N:8526	61		200873049	127618001	167285388	175434453	8526	SRX2209223	SRS1726584	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.89809	0.15716	0.84634	0.55363	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41359	41359	SRR4342167	SRX2209222	SRS1726583	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 2pos	GSM2334960		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:2	tbx5 2pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:2	GSM2334960	GSM2334960: tbx5 2pos; Danio rerio; RNA Seq	GSM2334960	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334960	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_2pos__HectorSanchez_RNA_Seq_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	721753525.0	11832025.0	GSM2334960 r1	0:61	A:210172867;C:139636671;G:184046654;T:187888215;N:9118	61		210172867	139636671	184046654	187888215	9118	SRX2209222	SRS1726583	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.88264	0.17411	0.85027	0.50468	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41360	41360	SRR4342166	SRX2209221	SRS1726581	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 2neg	GSM2334959		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:2	tbx5 2neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:2	GSM2334959	GSM2334959: tbx5 2neg; Danio rerio; RNA Seq	GSM2334959	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334959	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_2neg__HectorSanchez_RNA_Seq_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	719361654.0	11792814.0	GSM2334959 r1	0:61	A:210895656;C:137890002;G:180431743;T:190135096;N:9157	61		210895656	137890002	180431743	190135096	9157	SRX2209221	SRS1726581	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.76636	0.15624	0.8547	0.52604	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41361	41361	SRR4342165	SRX2209220	SRS1726582	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 10pos	GSM2334958		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:10	tbx5 10pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 positive ventricular cardiomyocytes\|pair:10	GSM2334958	GSM2334958: tbx5 10pos; Danio rerio; RNA Seq	GSM2334958	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334958	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_10pos__HectorSanchez_RNA_Seq_OvationSC_AAGCCT_L002_R1_001.fastq.gz	fastq	754707555.0	12372255.0	GSM2334958 r1	0:61	A:221942809;C:151029762;G:190399372;T:191312963;N:22649	61		221942809	151029762	190399372	191312963	22649	SRX2209220	SRS1726582	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.92066	0.11265	0.85121	0.57097	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41362	41362	SRR4342164	SRX2209219	SRS1726580	SRP090801	PRJNA345325	Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts	GSE87596	Transcriptome Analysis	In vertebrates the heart has two main layers of cardiac muscle a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.		pubmed:29382818		tbx5 10neg	GSM2334957		source name:Heart\|age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:10	tbx5 10neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	age:Adult\|tissue:Heart\|cell type:Tbx5 negative ventricular cardiomyocytes\|pair:10	GSM2334957	GSM2334957: tbx5 10neg; Danio rerio; RNA Seq	GSM2334957	1	RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. 4 biological replicates consisting of 5 pooled hearts were used per sample.	GEO Accession:GSM2334957	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP090801			tbx5_10neg__HectorSanchez_RNA_Seq_OvationSC_GTCGTA_L002_R1_001.fastq.gz	fastq	792684264.0	12994824.0	GSM2334957 r1	0:61	A:231862367;C:153096010;G:201328453;T:206373690;N:23744	61		231862367	153096010	201328453	206373690	23744	SRX2209219	SRS1726580	SRA481772	GEO	Bioinformatics Unit, CNIC	1	0.89586	0.16316	0.84435	0.53348	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2016-10-04	Adult	Adult	Heart	Cardiovascular System
41902	41902	SRR5337748	SRX2635098	SRS2043910	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS6	GSM2534771		tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS6	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534771	GSM2534771: YS6; Danio rerio; RNA Seq	GSM2534771	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534771	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS6_R1.fastq.gz	fastq	5434051896.0	43127396.0	GSM2534771 r1	0:126	A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089	126		1185876928	1354521221	1643633065	1249907593	113089	SRX2635098	SRS2043910	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.97351	0.17501	0.85303	0.75625	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41903	41903	SRR5337747	SRX2635097	SRS2043909	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS5	GSM2534770		tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS5	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534770	GSM2534770: YS5; Danio rerio; RNA Seq	GSM2534770	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534770	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS5_R1.fastq(1).gz	fastq	2297696058.0	18235683.0	GSM2534770 r1	0:126	A:648837532;C:505738661;G:568578688;T:574489076;N:52101	126		648837532	505738661	568578688	574489076	52101	SRX2635097	SRS2043909	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.94402	0.1927	0.77585	0.67728	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41904	41904	SRR5337746	SRX2635096	SRS2043908	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS4	GSM2534769		tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS4	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534769	GSM2534769: YS4; Danio rerio; RNA Seq	GSM2534769	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534769	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS4_R1.fastq.gz	fastq	4570634754.0	36274879.0	GSM2534769 r1	0:126	A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732	126		1179398927	1024363944	1239125274	1127644877	101732	SRX2635096	SRS2043908	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.93083	0.27465	0.78102	0.70638	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41905	41905	SRR5337745	SRX2635095	SRS2043907	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS3	GSM2534768		tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS3	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534768	GSM2534768: YS3; Danio rerio; RNA Seq	GSM2534768	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534768	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS3_R1.fastq.gz	fastq	5648398686.0	44828561.0	GSM2534768 r1	0:126	A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942	126		1607436982	1222995706	1369036558	1448805498	123942	SRX2635095	SRS2043907	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.93399	0.20266	0.78076	0.73978	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41906	41906	SRR5337744	SRX2635094	SRS2043906	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS2	GSM2534767		tissue:Mes1phros DL\|transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	YS2	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	Mesonephros DL		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh \|age:adult	GSM2534767	GSM2534767: YS2; Danio rerio; RNA Seq	GSM2534767	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534767	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS2_R1.fastq.gz	fastq	4680679374.0	37148249.0	GSM2534767 r1	0:126	A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709	126		1320151433	986429614	1112497899	1261495719	104709	SRX2635094	SRS2043906	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.91952	0.24724	0.73884	0.63985	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
41907	41907	SRR5337743	SRX2635093	SRS2043905	SRP101756	PRJNA378882	Transcriptome of the distal late segment of the zebrafish mesonephros	GSE96519	Transcriptome Analysis	We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.		pubmed:28656378		YS1	GSM2534766		tissue:DL segments\|transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	YS1	none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts	DL segments		DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.		transgene:Tgslc12a3:mCherry\|genotype:mCh+\|age:adult	GSM2534766	GSM2534766: YS1; Danio rerio; RNA Seq	GSM2534766	1	DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.	GEO Accession:GSM2534766	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP101756			20150717.A-YS1_R1.fastq.gz	fastq	7000703892.0	55561142.0	GSM2534766 r1	0:126	A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441	126		1521231890	1760818628	2148863730	1569634203	155441	SRX2635093	SRS2043905	SRA544882	GEO	Drummond, Nephrology, Massachusetts General Hospital	1	0.96016	0.1982	0.86261	0.75572	126	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only	United States	2017-03-12	Adult	Adult	Kidney	Renal System
42873	42873	SRR5817929	SRX2996183	SRS2347418	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 10	GSM2700316		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:10	neg 7dpi 10	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:10	GSM2700316	GSM2700316: neg 7dpi 10; Danio rerio; RNA Seq	GSM2700316	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700316	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_10__HS_OvationSC_ACCTCA_L001_R1_001.fastq.gz	fastq	2259317756.0	37037996.0	GSM2700316 r1	0:61	A:593901686;C:479409193;G:663867943;T:522077484;N:61450	61		593901686	479409193	663867943	522077484	61450	SRX2996183	SRS2347418	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.78451	0.21243	0.79275	0.70146	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42874	42874	SRR5817928	SRX2996182	SRS2347417	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 09	GSM2700315		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:9	neg 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:9	GSM2700315	GSM2700315: neg 7dpi 09; Danio rerio; RNA Seq	GSM2700315	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700315	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_09__HS_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	1969074205.0	32279905.0	GSM2700315 r1	0:61	A:506203021;C:400192379;G:588278464;T:474347230;N:53111	61		506203021	400192379	588278464	474347230	53111	SRX2996182	SRS2347417	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.83786	0.24573	0.78979	0.69734	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42875	42875	SRR5817927	SRX2996181	SRS2347416	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 08	GSM2700314		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:8	neg 7dpi 08	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:8	GSM2700314	GSM2700314: neg 7dpi 08; Danio rerio; RNA Seq	GSM2700314	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700314	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_08__HS_OvationSC_TCAGAG_L008_R1_001.fastq.gz	fastq	775093328.0	12706448.0	GSM2700314 r1	0:61	A:207451085;C:158380757;G:223015883;T:186233015;N:12588	61		207451085	158380757	223015883	186233015	12588	SRX2996181	SRS2347416	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.77247	0.24093	0.81142	0.61394	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42876	42876	SRR5817926	SRX2996180	SRS2347415	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 07	GSM2700313		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:7	neg 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:7	GSM2700313	GSM2700313: neg 7dpi 07; Danio rerio; RNA Seq	GSM2700313	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700313	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_07__HS_OvationSC_AGCATG_L008_R1_001.fastq.gz	fastq	667662873.0	10945293.0	GSM2700313 r1	0:61	A:184011441;C:129142619;G:186565080;T:167933144;N:10589	61		184011441	129142619	186565080	167933144	10589	SRX2996180	SRS2347415	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.78352	0.24932	0.79322	0.5843	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42877	42877	SRR5817925	SRX2996179	SRS2347414	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 06	GSM2700312		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:6	neg 7dpi 06	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:6	GSM2700312	GSM2700312: neg 7dpi 06; Danio rerio; RNA Seq	GSM2700312	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700312	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_06__HS_OvationSC_GTCGTA_L007_R1_001.fastq.gz	fastq	1506843472.0	24702352.0	GSM2700312 r1	0:61	A:415665970;C:284643457;G:414417308;T:391840093;N:276644	61		415665970	284643457	414417308	391840093	276644	SRX2996179	SRS2347414	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.67862	0.21798	0.79419	0.56611	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42878	42878	SRR5817924	SRX2996178	SRS2347412	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		neg 7dpi 05	GSM2700311		tissue:Heart\|cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:5	neg 7dpi 05	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry /postn:citrine \|treatment:7 xxx post injury\|pool:5	GSM2700311	GSM2700311: neg 7dpi 05; Danio rerio; RNA Seq	GSM2700311	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700311	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			Neg_7dpi_05__HS_OvationSC_ACCTCA_L007_R1_001.fastq.gz	fastq	1170594758.0	19190078.0	GSM2700311 r1	0:61	A:304620201;C:245838062;G:349652017;T:270272581;N:211897	61		304620201	245838062	349652017	270272581	211897	SRX2996178	SRS2347412	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.81997	0.21036	0.81962	0.66201	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42879	42879	SRR5817923	SRX2996177	SRS2347413	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		postnb citrine 7dpi 10	GSM2700310		tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:10	postnb citrine 7dpi 10	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:10	GSM2700310	GSM2700310: postnb citrine 7dpi 10; Danio rerio; RNA Seq	GSM2700310	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700310	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			postnb_7dpi_10__HS_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	2252204790.0	36921390.0	GSM2700310 r1	0:61	A:619277021;C:502942463;G:646027370;T:483900520;N:57416	61		619277021	502942463	646027370	483900520	57416	SRX2996177	SRS2347413	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.57676	0.1734	0.83984	0.65906	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42880	42880	SRR5817922	SRX2996176	SRS2347410	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		postnb citrine 7dpi 09	GSM2700309		tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:9	postnb citrine 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:9	GSM2700309	GSM2700309: postnb citrine 7dpi 09; Danio rerio; RNA Seq	GSM2700309	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700309	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			postnb_7dpi_09__HS_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	2283341264.0	37431824.0	GSM2700309 r1	0:61	A:647837199;C:525057060;G:652558979;T:457828691;N:59335	61		647837199	525057060	652558979	457828691	59335	SRX2996176	SRS2347410	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.51394	0.14658	0.85125	0.68998	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42881	42881	SRR5817921	SRX2996175	SRS2347411	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		postnb citrine 7dpi 07	GSM2700308		tissue:Heart\|cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:7	postnb citrine 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:postnb:citrine+\|treatment:7 xxx post injury\|pool:7	GSM2700308	GSM2700308: postnb citrine 7dpi 07; Danio rerio; RNA Seq	GSM2700308	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700308	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			postnb_7dpi_07__HS_OvationSC_GAGTCA_L008_R1_001.fastq.gz	fastq	722584040.0	11845640.0	GSM2700308 r1	0:61	A:200442958;C:161168985;G:204893226;T:156067063;N:11808	61		200442958	161168985	204893226	156067063	11808	SRX2996175	SRS2347411	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.50737	0.15544	0.85719	0.49067	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42882	42882	SRR5817920	SRX2996174	SRS2347409	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry 7dpi 09	GSM2700307		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	kdrl mCherry 7dpi 09	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:9	GSM2700307	GSM2700307: kdrl mCherry 7dpi 09; Danio rerio; RNA Seq	GSM2700307	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700307	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_7dpi_09__HS_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	2145360789.0	35169849.0	GSM2700307 r1	0:61	A:559652295;C:434757157;G:629761603;T:521131593;N:58141	61		559652295	434757157	629761603	521131593	58141	SRX2996174	SRS2347409	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.76139	0.25919	0.80608	0.67486	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42883	42883	SRR5817919	SRX2996173	SRS2347408	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry 7dpi 07	GSM2700306		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:7	kdrl mCherry 7dpi 07	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:7	GSM2700306	GSM2700306: kdrl mCherry 7dpi 07; Danio rerio; RNA Seq	GSM2700306	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700306	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_7dpi_07__HS_OvationSC_CGTAGA_L008_R1_001.fastq.gz	fastq	803488645.0	13171945.0	GSM2700306 r1	0:61	A:219205587;C:172957534;G:230065287;T:181248332;N:11905	61		219205587	172957534	230065287	181248332	11905	SRX2996173	SRS2347408	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.61434	0.19945	0.85242	0.62325	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42884	42884	SRR5817918	SRX2996172	SRS2347407	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry 7dpi 06	GSM2700305		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:6	kdrl mCherry 7dpi 06	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:6	GSM2700305	GSM2700305: kdrl mCherry 7dpi 06; Danio rerio; RNA Seq	GSM2700305	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700305	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_7dpi_06__HS_OvationSC_GGAGAA_L008_R1_001.fastq.gz	fastq	720805646.0	11816486.0	GSM2700305 r1	0:61	A:200358132;C:158104743;G:199543761;T:162788231;N:10779	61		200358132	158104743	199543761	162788231	10779	SRX2996172	SRS2347407	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.45356	0.17003	0.85137	0.56525	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42885	42885	SRR5817917	SRX2996171	SRS2347406	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry 7dpi 05	GSM2700304		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:5	kdrl mCherry 7dpi 05	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:7 xxx post injury\|pool:5	GSM2700304	GSM2700304: kdrl mCherry 7dpi 05; Danio rerio; RNA Seq	GSM2700304	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700304	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_7dpi_05__HS_OvationSC_AAGCCT_L007_R1_001.fastq.gz	fastq	1380653870.0	22633670.0	GSM2700304 r1	0:61	A:388484121;C:311044648;G:367785851;T:313097333;N:241917	61		388484121	311044648	367785851	313097333	241917	SRX2996171	SRS2347406	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.44514	0.18589	0.85569	0.53637	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42886	42886	SRR5817916	SRX2996170	SRS2347405	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry uninjured 04	GSM2700303		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:4	kdrl mCherry uninjured 04	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:4	GSM2700303	GSM2700303: kdrl mCherry uninjured 04; Danio rerio; RNA Seq	GSM2700303	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700303	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_uninj_04__HS_OvationSC_GCACTA_L007_R1_001.fastq.gz	fastq	1540717199.0	25257659.0	GSM2700303 r1	0:61	A:419376382;C:337803904;G:429107804;T:354151511;N:277598	61		419376382	337803904	429107804	354151511	277598	SRX2996170	SRS2347405	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.5821	0.21016	0.84904	0.6021	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42887	42887	SRR5817915	SRX2996169	SRS2347404	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry uninjured 03	GSM2700302		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:3	kdrl mCherry uninjured 03	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:3	GSM2700302	GSM2700302: kdrl mCherry uninjured 03; Danio rerio; RNA Seq	GSM2700302	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700302	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_uninj_03__HS_OvationSC_AGTGAG_L007_R1_001.fastq.gz	fastq	1258645879.0	20633539.0	GSM2700302 r1	0:61	A:349212875;C:258591407;G:348719714;T:301896773;N:225110	61		349212875	258591407	348719714	301896773	225110	SRX2996169	SRS2347404	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.59499	0.22916	0.83508	0.54761	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42888	42888	SRR5817914	SRX2996168	SRS2347403	SRP111552	PRJNA393857	Comparison of the expression profiles of kdrl:mCherry positive cells in injured versus uninjured zebrafish cardiac ventricle and analysis of the expression prolife of postnb:citrin positive cells upon injury compared to the rest of cardiac cells.	GSE101200	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the cardiac ventricular apex. Regeneration is preceed by a fibrotic response. To understand the contribution of different cell sources to zebrafish cardiac fibrosis we performed an RNASeq including endocardial kdrl:mCherry cells from an uninjured heart and activated endocardial kdrl:mCherry cells postnb:citrine fibroblasts and the rest of the cells at 7 xxx post injury. Overall design: Three to six biological replicates consisting of different cell types obtained from the ventricular apex.		pubmed:29610343		kdrl mCherry uninjured 02	GSM2700301		tissue:Heart\|cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:2	kdrl mCherry uninjured 02	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	Double transgenic postnb:citrine;kdrl:mCherry were cryoinjured or not as indicated.	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:kdrl:mCherry+\|treatment:Uninjured\|pool:2	GSM2700301	GSM2700301: kdrl mCherry uninjured 02; Danio rerio; RNA Seq	GSM2700301	1	3 5 pooled hearts were used per sample. Ventricular apexes were dissotiated with trypsin. mCherry positive and citrine positive cells were FAC sorted using SONY Synergy sy3200. RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700301	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111552			kdrl_uninj_02__HS_OvationSC_TGGTGA_L007_R1_001.fastq.gz	fastq	1339434096.0	21957936.0	GSM2700301 r1	0:61	A:368699684;C:287536628;G:376256631;T:306701372;N:239781	61		368699684	287536628	376256631	306701372	239781	SRX2996168	SRS2347403	SRA585701	GEO	Bioinformatics Unit, CNIC	1	0.41301	0.17019	0.85458	0.5146	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42889	42889	SRR5818018	SRX2996265	SRS2347497	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 4 pos	GSM2700333		tissue:Heart\|cell type:wt1a+\|pool:4	wt1aGFP 4 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:4	GSM2700333	GSM2700333: wt1aGFP 4 pos; Danio rerio; RNA Seq	GSM2700333	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700333	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_34_pos__HS_RNA_Seq_OvationSC_GTCGTA_L001_R1_001.fastq.gz	fastq	723314759.0	11857619.0	GSM2700333 r1	0:61	A:201917485;C:141523845;G:184676365;T:195150579;N:46485	61		201917485	141523845	184676365	195150579	46485	SRX2996265	SRS2347497	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82231	0.30947	0.80137	0.55406	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42890	42890	SRR5818019	SRX2996265	SRS2347497	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 4 pos	GSM2700333		tissue:Heart\|cell type:wt1a+\|pool:4	wt1aGFP 4 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:4	GSM2700333	GSM2700333: wt1aGFP 4 pos; Danio rerio; RNA Seq	GSM2700333	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700333	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_34_pos__HS_RNA_Seq_OvationSC_GTCGTA_L002_R1_001.fastq.gz	fastq	736427807.0	12072587.0	GSM2700333 r2	0:61	A:205663718;C:144074430;G:188007794;T:198654037;N:27828	61		205663718	144074430	188007794	198654037	27828	SRX2996265	SRS2347497	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82156	0.3081	0.80107	0.55258	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42891	42891	SRR5818016	SRX2996264	SRS2347496	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 4 neg	GSM2700332		tissue:Heart\|cell type:wt1a \|pool:4	wt1aGFP 4 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:4	GSM2700332	GSM2700332: wt1aGFP 4 neg; Danio rerio; RNA Seq	GSM2700332	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700332	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_34_neg__HS_RNA_Seq_OvationSC_AAGCCT_L001_R1_001.fastq.gz	fastq	845878277.0	13866857.0	GSM2700332 r1	0:61	A:249667621;C:171998644;G:210584175;T:213573132;N:54705	61		249667621	171998644	210584175	213573132	54705	SRX2996264	SRS2347496	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90245	0.18824	0.81793	0.69585	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42892	42892	SRR5818017	SRX2996264	SRS2347496	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 4 neg	GSM2700332		tissue:Heart\|cell type:wt1a \|pool:4	wt1aGFP 4 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:4	GSM2700332	GSM2700332: wt1aGFP 4 neg; Danio rerio; RNA Seq	GSM2700332	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700332	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_34_neg__HS_RNA_Seq_OvationSC_AAGCCT_L002_R1_001.fastq.gz	fastq	862736664.0	14143224.0	GSM2700332 r2	0:61	A:254822084;C:175437676;G:214663386;T:217781386;N:32132	61		254822084	175437676	214663386	217781386	32132	SRX2996264	SRS2347496	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90087	0.1871	0.81779	0.68372	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42893	42893	SRR5818014	SRX2996263	SRS2347495	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 3 pos	GSM2700331		tissue:Heart\|cell type:wt1a+\|pool:3	wt1aGFP 3 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:3	GSM2700331	GSM2700331: wt1aGFP 3 pos; Danio rerio; RNA Seq	GSM2700331	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700331	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_33_pos__HS_RNA_Seq_OvationSC_GTGCTT_L001_R1_001.fastq.gz	fastq	774308441.0	12693581.0	GSM2700331 r1	0:61	A:214992220;C:150401431;G:203530010;T:205334623;N:50157	61		214992220	150401431	203530010	205334623	50157	SRX2996263	SRS2347495	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.85135	0.30434	0.79859	0.56227	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42894	42894	SRR5818015	SRX2996263	SRS2347495	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 3 pos	GSM2700331		tissue:Heart\|cell type:wt1a+\|pool:3	wt1aGFP 3 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:3	GSM2700331	GSM2700331: wt1aGFP 3 pos; Danio rerio; RNA Seq	GSM2700331	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700331	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_33_pos__HS_RNA_Seq_OvationSC_GTGCTT_L002_R1_001.fastq.gz	fastq	785516154.0	12877314.0	GSM2700331 r2	0:61	A:218236052;C:152511901;G:206411606;T:208326427;N:30168	61		218236052	152511901	206411606	208326427	30168	SRX2996263	SRS2347495	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.85177	0.30473	0.80081	0.56348	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42895	42895	SRR5818012	SRX2996262	SRS2347494	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 3 neg	GSM2700330		tissue:Heart\|cell type:wt1a \|pool:3	wt1aGFP 3 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:3	GSM2700330	GSM2700330: wt1aGFP 3 neg; Danio rerio; RNA Seq	GSM2700330	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700330	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_33_neg__HS_RNA_Seq_OvationSC_ACCTCA_L001_R1_001.fastq.gz	fastq	725733470.0	11897270.0	GSM2700330 r1	0:61	A:216602034;C:144864671;G:177825033;T:186394034;N:47698	61		216602034	144864671	177825033	186394034	47698	SRX2996262	SRS2347494	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.89906	0.20936	0.81264	0.69072	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42896	42896	SRR5818013	SRX2996262	SRS2347494	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 3 neg	GSM2700330		tissue:Heart\|cell type:wt1a \|pool:3	wt1aGFP 3 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:3	GSM2700330	GSM2700330: wt1aGFP 3 neg; Danio rerio; RNA Seq	GSM2700330	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700330	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_33_neg__HS_RNA_Seq_OvationSC_ACCTCA_L002_R1_001.fastq.gz	fastq	739526485.0	12123385.0	GSM2700330 r2	0:61	A:220804426;C:147618040;G:181199008;T:189877408;N:27603	61		220804426	147618040	181199008	189877408	27603	SRX2996262	SRS2347494	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.89897	0.20803	0.8126	0.68941	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42897	42897	SRR5818010	SRX2996261	SRS2347493	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 2 pos	GSM2700329		tissue:Heart\|cell type:wt1a+\|pool:2	wt1aGFP 2 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:2	GSM2700329	GSM2700329: wt1aGFP 2 pos; Danio rerio; RNA Seq	GSM2700329	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700329	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_32_pos__HS_RNA_Seq_OvationSC_GCACTA_L001_R1_001.fastq.gz	fastq	754469960.0	12368360.0	GSM2700329 r1	0:61	A:212826941;C:144472909;G:187613892;T:209506276;N:49942	61		212826941	144472909	187613892	209506276	49942	SRX2996261	SRS2347493	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82785	0.31821	0.79113	0.57087	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42898	42898	SRR5818011	SRX2996261	SRS2347493	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 2 pos	GSM2700329		tissue:Heart\|cell type:wt1a+\|pool:2	wt1aGFP 2 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:2	GSM2700329	GSM2700329: wt1aGFP 2 pos; Danio rerio; RNA Seq	GSM2700329	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700329	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_32_pos__HS_RNA_Seq_OvationSC_GCACTA_L002_R1_001.fastq.gz	fastq	768777327.0	12602907.0	GSM2700329 r2	0:61	A:216934227;C:147173989;G:191157153;T:213483110;N:28848	61		216934227	147173989	191157153	213483110	28848	SRX2996261	SRS2347493	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82552	0.31671	0.79088	0.50918	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42899	42899	SRR5818008	SRX2996260	SRS2347491	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 2 neg	GSM2700328		tissue:Heart\|cell type:wt1a \|pool:2	wt1aGFP 2 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:2	GSM2700328	GSM2700328: wt1aGFP 2 neg; Danio rerio; RNA Seq	GSM2700328	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700328	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_32_neg__HS_RNA_Seq_OvationSC_AGTGAG_L001_R1_001.fastq.gz	fastq	692638530.0	11354730.0	GSM2700328 r1	0:61	A:211149267;C:142433123;G:165634275;T:173375719;N:46146	61		211149267	142433123	165634275	173375719	46146	SRX2996260	SRS2347491	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.91099	0.17805	0.81458	0.72923	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42900	42900	SRR5818009	SRX2996260	SRS2347491	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 2 neg	GSM2700328		tissue:Heart\|cell type:wt1a \|pool:2	wt1aGFP 2 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:2	GSM2700328	GSM2700328: wt1aGFP 2 neg; Danio rerio; RNA Seq	GSM2700328	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700328	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_32_neg__HS_RNA_Seq_OvationSC_AGTGAG_L002_R1_001.fastq.gz	fastq	704040406.0	11541646.0	GSM2700328 r2	0:61	A:214725213;C:144725366;G:168345724;T:176217859;N:26244	61		214725213	144725366	168345724	176217859	26244	SRX2996260	SRS2347491	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.90997	0.17763	0.81527	0.72316	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42901	42901	SRR5818006	SRX2996259	SRS2347492	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 1 pos	GSM2700327		tissue:Heart\|cell type:wt1a+\|pool:1	wt1aGFP 1 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:1	GSM2700327	GSM2700327: wt1aGFP 1 pos; Danio rerio; RNA Seq	GSM2700327	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700327	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_31_pos__HS_RNA_Seq_OvationSC_TGGTGA_L001_R1_001.fastq.gz	fastq	729643509.0	11961369.0	GSM2700327 r1	0:61	A:209109414;C:140044116;G:176769088;T:203672961;N:47930	61		209109414	140044116	176769088	203672961	47930	SRX2996259	SRS2347492	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.82015	0.30797	0.79748	0.46884	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42902	42902	SRR5818007	SRX2996259	SRS2347492	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 1 pos	GSM2700327		tissue:Heart\|cell type:wt1a+\|pool:1	wt1aGFP 1 pos	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a+\|pool:1	GSM2700327	GSM2700327: wt1aGFP 1 pos; Danio rerio; RNA Seq	GSM2700327	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700327	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_31_pos__HS_RNA_Seq_OvationSC_TGGTGA_L002_R1_001.fastq.gz	fastq	743468183.0	12188003.0	GSM2700327 r2	0:61	A:213138374;C:142664132;G:180105124;T:207532889;N:27664	61		213138374	142664132	180105124	207532889	27664	SRX2996259	SRS2347492	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.81957	0.30392	0.79527	0.47293	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42903	42903	SRR5818004	SRX2996258	SRS2347490	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 1 neg	GSM2700326		tissue:Heart\|cell type:wt1a \|pool:1	wt1aGFP 1 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:1	GSM2700326	GSM2700326: wt1aGFP 1 neg; Danio rerio; RNA Seq	GSM2700326	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700326	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_31_neg__HS_RNA_Seq_OvationSC_AACCAG_L001_R1_001.fastq.gz	fastq	830080436.0	13607876.0	GSM2700326 r1	0:61	A:251391883;C:167411203;G:203106619;T:208117027;N:53704	61		251391883	167411203	203106619	208117027	53704	SRX2996258	SRS2347490	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.88568	0.18069	0.82298	0.729	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42904	42904	SRR5818005	SRX2996258	SRS2347490	SRP111553	PRJNA393878	Comparison of the expression profile of GFP positive cells from Tg 6.8wt1a:EGFP with the rest of the cells in adult zebrafish cardiac ventricles	GSE101204	Transcriptome Analysis	wt1a:GFP labels a population of subepicardial cells in the uninjured ventricle. Here we compare the expression profile of wt1a:GFP positive cells to the rest of the cells of the ventricle. Overall design: Four paired biological replicates of wt1a:GFP positive and wt1a:GFP negative cells obtained from pools of 3 5 zebrafish heart ventricles.		pubmed:29610343		wt1aGFP 1 neg	GSM2700326		tissue:Heart\|cell type:wt1a \|pool:1	wt1aGFP 1 neg	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: matrix counts.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	No treatment was applied.	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	cell type:wt1a \|pool:1	GSM2700326	GSM2700326: wt1aGFP 1 neg; Danio rerio; RNA Seq	GSM2700326	1	Whole zebrafish heart ventricles were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700326	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111553			wt1aV_31_neg__HS_RNA_Seq_OvationSC_AACCAG_L002_R1_001.fastq.gz	fastq	841688675.0	13798175.0	GSM2700326 r2	0:61	A:255002009;C:169696986;G:205887037;T:211071121;N:31522	61		255002009	169696986	205887037	211071121	31522	SRX2996258	SRS2347490	SRA585736	GEO	Bioinformatics Unit, CNIC	1	0.88535	0.18061	0.82199	0.73203	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42905	42905	SRR5820065	SRX2997963	SRS2349071	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 4	GSM2700300		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700300	GSM2700300: postnbCreERT2 60dpi 4; Danio rerio; RNA Seq	GSM2700300	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700300	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_24__HS_RNA_Seq_OvationSC_TTGGCA_L001_R1_001.fastq.gz	fastq	658472125.0	10794625.0	GSM2700300 r1										SRX2997963	SRS2349071	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.81414	0.33277	0.81746	0.52723	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42906	42906	SRR5820066	SRX2997963	SRS2349071	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 4	GSM2700300		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700300	GSM2700300: postnbCreERT2 60dpi 4; Danio rerio; RNA Seq	GSM2700300	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700300	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_24__HS_RNA_Seq_OvationSC_TTGGCA_L002_R1_001.fastq.gz	fastq	667651710.0	10945110.0	GSM2700300 r2	0:61	A:187398827;C:124387075;G:170371629;T:185469418;N:24761	61		187398827	124387075	170371629	185469418	24761	SRX2997963	SRS2349071	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.81012	0.32665	0.82207	0.52786	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42907	42907	SRR5820063	SRX2997962	SRS2349070	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 2	GSM2700299		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700299	GSM2700299: postnbCreERT2 60dpi 2; Danio rerio; RNA Seq	GSM2700299	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700299	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_22__HS_RNA_Seq_OvationSC_TCAGAG_L001_R1_001.fastq.gz	fastq	812209022.0	13314902.0	GSM2700299 r1	0:61	A:228658409;C:151594988;G:205412898;T:226488086;N:54641	61		228658409	151594988	205412898	226488086	54641	SRX2997962	SRS2349070	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84081	0.33669	0.80026	0.55189	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42908	42908	SRR5820064	SRX2997962	SRS2349070	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 2	GSM2700299		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700299	GSM2700299: postnbCreERT2 60dpi 2; Danio rerio; RNA Seq	GSM2700299	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700299	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_22__HS_RNA_Seq_OvationSC_TCAGAG_L002_R1_001.fastq.gz	fastq	824141232.0	13510512.0	GSM2700299 r2	0:61	A:232162664;C:153749805;G:208354200;T:229843231;N:31332	61		232162664	153749805	208354200	229843231	31332	SRX2997962	SRS2349070	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.83912	0.33627	0.79935	0.55638	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42909	42909	SRR5820061	SRX2997961	SRS2349069	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 1	GSM2700298		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700298	GSM2700298: postnbCreERT2 60dpi 1; Danio rerio; RNA Seq	GSM2700298	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700298	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_21__HS_RNA_Seq_OvationSC_CGTAGA_L001_R1_001.fastq.gz	fastq	820312811.0	13447751.0	GSM2700298 r1	0:61	A:224903496;C:155230235;G:218395518;T:221729453;N:54109	61		224903496	155230235	218395518	221729453	54109	SRX2997961	SRS2349069	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82352	0.30266	0.7936	0.54956	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42910	42910	SRR5820062	SRX2997961	SRS2349069	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 60dpi 1	GSM2700298		tissue:Heart\|treatment:60 dpi	postnbCreERT2 60dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:60 dpi	GSM2700298	GSM2700298: postnbCreERT2 60dpi 1; Danio rerio; RNA Seq	GSM2700298	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700298	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC60dpi_21__HS_RNA_Seq_OvationSC_CGTAGA_L002_R1_001.fastq.gz	fastq	831069612.0	13624092.0	GSM2700298 r2	0:61	A:227982894;C:157205567;G:221135004;T:224715301;N:30846	61		227982894	157205567	221135004	224715301	30846	SRX2997961	SRS2349069	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82359	0.30223	0.79876	0.5386	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42911	42911	SRR5820059	SRX2997960	SRS2349068	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 4	GSM2700297		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700297	GSM2700297: postnbCreERT2 7dpi 4; Danio rerio; RNA Seq	GSM2700297	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700297	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_24__HS_RNA_Seq_OvationSC_GAGTCA_L001_R1_001.fastq.gz	fastq	529129067.0	8674247.0	GSM2700297 r1	0:61	A:145838822;C:101005915;G:133827073;T:148422408;N:34849	61		145838822	101005915	133827073	148422408	34849	SRX2997960	SRS2349068	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85327	0.29887	0.82398	0.59536	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42912	42912	SRR5820060	SRX2997960	SRS2349068	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 4	GSM2700297		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700297	GSM2700297: postnbCreERT2 7dpi 4; Danio rerio; RNA Seq	GSM2700297	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700297	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_24__HS_RNA_Seq_OvationSC_GAGTCA_L002_R1_001.fastq.gz	fastq	537096033.0	8804853.0	GSM2700297 r2	0:61	A:148103577;C:102498850;G:135735762;T:150738056;N:19788	61		148103577	102498850	135735762	150738056	19788	SRX2997960	SRS2349068	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85107	0.29724	0.82489	0.59155	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42913	42913	SRR5820057	SRX2997959	SRS2349067	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 3	GSM2700296		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 3	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700296	GSM2700296: postnbCreERT2 7dpi 3; Danio rerio; RNA Seq	GSM2700296	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700296	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_23__HS_RNA_Seq_OvationSC_AGCATG_L001_R1_001.fastq.gz	fastq	732770857.0	12012637.0	GSM2700296 r1	0:61	A:202857149;C:140357985;G:191010203;T:198497101;N:48419	61		202857149	140357985	191010203	198497101	48419	SRX2997959	SRS2349067	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84025	0.28858	0.78297	0.58582	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42914	42914	SRR5820058	SRX2997959	SRS2349067	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 3	GSM2700296		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 3	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700296	GSM2700296: postnbCreERT2 7dpi 3; Danio rerio; RNA Seq	GSM2700296	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700296	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_23__HS_RNA_Seq_OvationSC_AGCATG_L002_R1_001.fastq.gz	fastq	742926320.0	12179120.0	GSM2700296 r2	0:61	A:205824167;C:142245364;G:193518156;T:201311005;N:27628	61		205824167	142245364	193518156	201311005	27628	SRX2997959	SRS2349067	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.83963	0.28878	0.78577	0.57339	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42915	42915	SRR5820055	SRX2997958	SRS2349066	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 2	GSM2700295		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700295	GSM2700295: postnbCreERT2 7dpi 2; Danio rerio; RNA Seq	GSM2700295	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700295	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_22__HS_RNA_Seq_OvationSC_GGAGAA_L001_R1_001.fastq.gz	fastq	798125708.0	13084028.0	GSM2700295 r1	0:61	A:220033386;C:154219970;G:209254999;T:214564836;N:52517	61		220033386	154219970	209254999	214564836	52517	SRX2997958	SRS2349066	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.84868	0.29566	0.78395	0.60892	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42916	42916	SRR5820056	SRX2997958	SRS2349066	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 2	GSM2700295		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700295	GSM2700295: postnbCreERT2 7dpi 2; Danio rerio; RNA Seq	GSM2700295	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700295	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_22__HS_RNA_Seq_OvationSC_GGAGAA_L002_R1_001.fastq.gz	fastq	811023060.0	13295460.0	GSM2700295 r2	0:61	A:223729714;C:156680800;G:212510056;T:218071242;N:31248	61		223729714	156680800	212510056	218071242	31248	SRX2997958	SRS2349066	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.85147	0.29531	0.78614	0.59452	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42917	42917	SRR5820053	SRX2997957	SRS2349065	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 1	GSM2700294		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700294	GSM2700294: postnbCreERT2 7dpi 1; Danio rerio; RNA Seq	GSM2700294	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700294	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_21__HS_RNA_Seq_OvationSC_AAGAGG_L001_R1_001.fastq.gz	fastq	791727113.0	12979133.0	GSM2700294 r1	0:61	A:221474690;C:149322441;G:203129939;T:217747332;N:52711	61		221474690	149322441	203129939	217747332	52711	SRX2997957	SRS2349065	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82196	0.30812	0.7895	0.58101	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
42918	42918	SRR5820054	SRX2997957	SRS2349065	SRP111705	PRJNA393987	postnb lineage traced cells at 7 and 60 days post cryoinjury dpi during adult zebrafish cardiac ventricle regeneration	GSE101199	Transcriptome Analysis	Contrary to mammals zebrafish regenerate their heart upon cryoinjury of the ventricular apex. Regeneration is preceeded by a transient fibrotic response. Here we compare the expression profile of fibroblast like cells at 7 different time points of fibrosis resolution. Using a postnb:CreERT2; ubb:loxP GFP loxP mCherrycz1701 double transgenic line we permanently label cells that expressed postnb at 3 and 4 xxx post injury dpi with mCherry by administration of 4 OHT. We sequenced mCherry labelled cells obtained from the ventricular apex at 7 and 60 dpi. Overall design: postnb derived cells were FAC sorted from a pool of three to five biological samples. Four pools were collected at 7 dpi and three at 60 dpi. RNA was extracted from those pools and further processed for transcriptome analysis.		pubmed:29610343		postnbCreERT2 7dpi 1	GSM2700294		tissue:Heart\|treatment:7 dpi	postnbCreERT2 7dpi 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.25. Genome build: Ensembl genebuild 10 release 82 Danio rerio assembly Zv9. Supplementary files format and content: Matrix table.xlsx file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.	Heart	postnb:CreERT2;ubb:loxP GFP loxP mCherry fish were treated over night with 4 OHT 10 µM at 3 and 4 dpi. Fish were dissected at 7 or 60 dpi.	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	All experiments were conducted with adult zebrafish between 3 month and 9 month of age raised at a density of 3 fish/l.	treatment:7 dpi	GSM2700294	GSM2700294: postnbCreERT2 7dpi 1; Danio rerio; RNA Seq	GSM2700294	1	Ventricular apex were dissotiated using pronase elastase DNase and liberase TH. mCherry positive cells were FAC sorted ventricular apex. Cells were sorted using SONY Synergy sy3200 and RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions.0.2 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification. The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit® fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads. FastQ files for each sample were obtained using CASAVA v1.8 software Illumina. 3 5 pooled hearts were used per sample. Index tagged cDNA libraries were constructed with the TruSeq RNA Sample Preparation v2 Kit Illumina San Diego CA.	GEO Accession:GSM2700294	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP111705			pstnC7dpi_21__HS_RNA_Seq_OvationSC_AAGAGG_L002_R1_001.fastq.gz	fastq	801987435.0	13147335.0	GSM2700294 r2	0:61	A:224436021;C:151157500;G:205611822;T:220752212;N:29880	61		224436021	151157500	205611822	220752212	29880	SRX2997957	SRS2349065	SRA586092	GEO	Bioinformatics Unit, CNIC	1	0.82242	0.30689	0.79044	0.57309	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2017-07-11	Adult	Adult	Heart	Cardiovascular System
48425	48425	SRR7266726	SRX4170565	SRS3382375	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MRWT1 5	GSM3177088		tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	MRWT1 5	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	GSM3177088	GSM3177088: MRWT1 5; Danio rerio; RNA Seq	GSM3177088	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177088	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MRWT15__AnaBelenGarcia_RNA_Seq_OvationSC_GAGTCA_L002_R1_001.fastq.gz	fastq	1609149012.0	26379492.0	GSM3177088 r1	0:61 1:0	A:432557422;C:346615764;G:438332984;T:391553708;N:89134	61	0	432557422	346615764	438332984	391553708	89134	SRX4170565	SRS3382375	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.75712	0.25964	0.83737	0.58775	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48426	48426	SRR7266725	SRX4170564	SRS3382374	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MRWT1 4	GSM3177087		tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	MRWT1 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:2	GSM3177087	GSM3177087: MRWT1 4; Danio rerio; RNA Seq	GSM3177087	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177087	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MRWT14__AnaBelenGarcia_RNA_Seq_OvationSC_AGCATG_L002_R1_001.fastq.gz	fastq	1578335899.0	25874359.0	GSM3177087 r1	0:61 1:0	A:403622771;C:331438424;G:444808774;T:398377182;N:88748	61	0	403622771	331438424	444808774	398377182	88748	SRX4170564	SRS3382374	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.87043	0.29681	0.84376	0.60111	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48427	48427	SRR7266724	SRX4170563	SRS3382372	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MRWT1 2	GSM3177086		tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	MRWT1 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	GSM3177086	GSM3177086: MRWT1 2; Danio rerio; RNA Seq	GSM3177086	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177086	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MRWT1_2__AnaBelenGarcia_RNA_Seq_OvationSC_CACAGT_L001_R1_001.fastq.gz	fastq	1647958920.0	27465982.0	GSM3177086 r1	0:60	A:443708613;C:313933032;G:445835945;T:444367644;N:113686	60		443708613	313933032	445835945	444367644	113686	SRX4170563	SRS3382372	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.85143	0.29582	0.83564	0.59274	60	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48428	48428	SRR7266723	SRX4170562	SRS3382373	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MRWT1 1	GSM3177085		tissue:mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts\|phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	MRWT1 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry/wt1b:eGFP cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry/wt1b:eGFP\|library batch:1	GSM3177085	GSM3177085: MRWT1 1; Danio rerio; RNA Seq	GSM3177085	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177085	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MRWT1_1__AnaBelenGarcia_RNA_Seq_OvationSC_TCAGAG_L001_R1_001.fastq.gz	fastq	1361787360.0	22696456.0	GSM3177085 r1	0:60	A:365235306;C:266923973;G:370787525;T:358747902;N:92654	60		365235306	266923973	370787525	358747902	92654	SRX4170562	SRS3382373	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.79693	0.28628	0.87903	0.55995	60	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48429	48429	SRR7266722	SRX4170561	SRS3382371	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MR 5	GSM3177084		tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:2	MR 5	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:2	GSM3177084	GSM3177084: MR 5; Danio rerio; RNA Seq	GSM3177084	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177084	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MR5__AnaBelenGarcia_RNA_Seq_OvationSC_GGAGAA_L002_R1_001.fastq.gz	fastq	1159385276.0	19006316.0	GSM3177084 r1	0:61 1:0	A:316084223;C:249253761;G:317016302;T:276966251;N:64739	61	0	316084223	249253761	317016302	276966251	64739	SRX4170561	SRS3382371	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.72668	0.26774	0.84078	0.56426	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48430	48430	SRR7266721	SRX4170560	SRS3382369	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MR 4	GSM3177083		tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:2	MR 4	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:2	GSM3177083	GSM3177083: MR 4; Danio rerio; RNA Seq	GSM3177083	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177083	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MR4__AnaBelenGarcia_RNA_Seq_OvationSC_AAGAGG_L002_R1_001.fastq.gz	fastq	1031492188.0	16909708.0	GSM3177083 r1	0:61 1:0	A:275201446;C:215010611;G:277227531;T:263995484;N:57116	61	0	275201446	215010611	277227531	263995484	57116	SRX4170560	SRS3382369	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.8243	0.31617	0.83883	0.54481	61	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48431	48431	SRR7266720	SRX4170559	SRS3382370	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MR 2	GSM3177082		tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:1	MR 2	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:1	GSM3177082	GSM3177082: MR 2; Danio rerio; RNA Seq	GSM3177082	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177082	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MR2__AnaBelenGarcia_RNA_Seq_OvationSC_GAGTCA_L001_R1_001.fastq.gz	fastq	1423227000.0	23720450.0	GSM3177082 r1	0:60	A:409084360;C:294887211;G:360615674;T:358543749;N:96006	60		409084360	294887211	360615674	358543749	96006	SRX4170559	SRS3382370	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.65591	0.26043	0.82041	0.62336	60	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
48432	48432	SRR7266719	SRX4170558	SRS3382368	SRP149832	PRJNA474730	Transcriptome analysis of wt1b:eGFP positive macrophages in the regenerating zebrafish heart	GSE115381	Transcriptome Analysis	Little is known about zebrafish macrophage subtypes and their contribution to organ regeneration. Using the transgenic line wt1b:eGFP we identified a subtype of macrophages in the regenerating heart that is transcriptionally different from the rest of macrophages. Overall design: Hearts from Tgwt1b:eGFP; mpeg1:mCherry zebrafish were cryoinjured and at 4 dpi mCherry and GFP/mCherry cells were FAC sorted. RNA was extracted from 4 pools of GFP/mCherry and 4 pools of mCherry single positive cells and RNAseq was performed.	parent bioproject:PRJNA485878	pubmed:31365871		MR 1	GSM3177081		tissue:mpeg1:mCherry cells from 4dpi hearts\|phenotype:mpeg1:mCherry\|library batch:1	MR 1	Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM normalized batch corrected counts per million for each sample.	mpeg1:mCherry cells from 4dpi hearts	Four biological replicates consisting of FAC sorted cells coming from five to seven pooled hearts were used per phenotype.	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	All experiments were conducted with adult zebrafish between 6 month and 9 month of age raised at a density of 3 fish/l.	phenotype:mpeg1:mCherry\|library batch:1	GSM3177081	GSM3177081: MR 1; Danio rerio; RNA Seq	GSM3177081	1	RNA was extracted with PicoPure™ RNA Isolation Kit Index tagged cDNA libraries were constructed in two batches from total RNA 1 ng with the TruSeq RNA sample preparation v2 kit Illumina post amplification with the NuGen OvationSC RNA Seq System. Quality quantity and size distribution of the Illumina libraries were determined using the DNA 1000 kit Agilent Bioanalyzer. RNASeq. Libraries were sequenced single end mode and length of 60 61 bp on the Illumina HiSeq 2500 system using the standard RNA sequencing protocol in the TruSeq SBS kit v5.	GEO Accession:GSM3177081	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP149832			MR1__AnaBelenGarcia_RNA_Seq_OvationSC_AGCATG_L001_R1_001.fastq.gz	fastq	1634874420.0	27247907.0	GSM3177081 r1	0:60	A:466410867;C:312698413;G:414814899;T:440838061;N:112180	60		466410867	312698413	414814899	440838061	112180	SRX4170558	SRS3382368	SRA715602	GEO	Bioinformatics Unit, CNIC	1	0.20756	0.07949	0.90019	0.64646	60	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	sc_generic	single_cell_generic	generic-scrnaseq-only	Spain	2018-06-05	Adult	Adult	Heart	Cardiovascular System
54345	54345	SRR10126111	SRX6854760	SRS5392962	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG 1 01 E02	GSM4080997		tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0813302707773932	RG 1 01 E02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.0813302707773932	GSM4080997	GSM4080997: RG 1 01 E02; Danio rerio; RNA Seq	GSM4080997	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080997	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L23839_RG_1_01_E02.bam	bam	16444652.0	216377.0	GSM4080997 r1	0:76	A:4583352;C:3984328;G:3906383;T:3970500;N:89	76		4583352	3984328	3906383	3970500	89	SRX6854760	SRS5392962	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.26908	0.09242	0.99825	0.67661	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54346	54346	SRR10126110	SRX6854759	SRS5392961	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG 1 01 B02	GSM4080996		tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.137111856361026	RG 1 01 B02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.137111856361026	GSM4080996	GSM4080996: RG 1 01 B02; Danio rerio; RNA Seq	GSM4080996	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080996	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L23836_RG_1_01_B02.bam	bam	14345076.0	188751.0	GSM4080996 r1	0:76	A:4237579;C:3235570;G:3240300;T:3631525;N:102	76		4237579	3235570	3240300	3631525	102	SRX6854759	SRS5392961	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.37026	0.12862	0.99805	0.83484	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54347	54347	SRR10126109	SRX6854758	SRS5392960	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG 1 01 C01	GSM4080995		tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.596981146320204	RG 1 01 C01	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.596981146320204	GSM4080995	GSM4080995: RG 1 01 C01; Danio rerio; RNA Seq	GSM4080995	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080995	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L23829_RG_1_01_C01_mod.bam	bam	44287252.0	582727.0	GSM4080995 r1	0:76	A:12057290;C:10158222;G:10161190;T:11910345;N:205	76		12057290	10158222	10161190	11910345	205	SRX6854758	SRS5392960	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.83606	0.11078	0.97364	0.51554	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54348	54348	SRR10126108	SRX6854757	SRS5392959	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG 1 01 G02	GSM4080994		tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.336437957921624	RG 1 01 G02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.336437957921624	GSM4080994	GSM4080994: RG 1 01 G02; Danio rerio; RNA Seq	GSM4080994	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080994	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L23841_RG_1_01_G02_mod.bam	bam	18090356.0	238031.0	GSM4080994 r1	0:76	A:5124071;C:4154073;G:4123933;T:4688206;N:73	76		5124071	4154073	4123933	4688206	73	SRX6854757	SRS5392959	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.63512	0.05239	0.99257	0.67835	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54349	54349	SRR10126107	SRX6854756	SRS5392958	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG 1 01 F02	GSM4080993		tissue:Brain\|sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.169583947726024	RG 1 01 F02	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx855 01\|batch:bfx855\|fraction mapped:0.169583947726024	GSM4080993	GSM4080993: RG 1 01 F02; Danio rerio; RNA Seq	GSM4080993	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080993	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L23840_RG_1_01_F02.bam	bam	13143060.0	172935.0	GSM4080993 r1	0:76	A:3676240;C:3051166;G:3081467;T:3334128;N:59	76		3676240	3051166	3081467	3334128	59	SRX6854756	SRS5392958	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.4252	0.0971	0.99697	0.81536	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54350	54350	SRR10126106	SRX6854755	SRS5392957	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON30 01 F12	GSM4080992		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.307951918399687	ON30 01 F12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.307951918399687	GSM4080992	GSM4080992: ON30 01 F12; Danio rerio; RNA Seq	GSM4080992	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080992	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22296_ON30_01_F12_mod.bam	bam	45464644.0	598219.0	GSM4080992 r1	0:76	A:13070969;C:9463048;G:9617299;T:13313099;N:229	76		13070969	9463048	9617299	13313099	229	SRX6854755	SRS5392957	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85125	0.28428	0.94795	0.49176	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54351	54351	SRR10126105	SRX6854754	SRS5392956	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		RG31 01 H12	GSM4080991		tissue:Brain\|sorting:RG\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.349622553699452	RG31 01 H12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:RG\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.349622553699452	GSM4080991	GSM4080991: RG31 01 H12; Danio rerio; RNA Seq	GSM4080991	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080991	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22298_RG31_01_H12_mod.bam	bam	54043448.0	711098.0	GSM4080991 r1	0:76	A:14990424;C:11836357;G:12008841;T:15207589;N:237	76		14990424	11836357	12008841	15207589	237	SRX6854754	SRS5392956	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.85818	0.139	0.95706	0.49646	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54352	54352	SRR10126104	SRX6854753	SRS5392955	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON29 01 E12	GSM4080990		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.270605518893939	ON29 01 E12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.270605518893939	GSM4080990	GSM4080990: ON29 01 E12; Danio rerio; RNA Seq	GSM4080990	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080990	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22295_ON29_01_E12_mod.bam	bam	31968716.0	420641.0	GSM4080990 r1	0:76	A:9066610;C:6733147;G:6934070;T:9234786;N:103	76		9066610	6733147	6934070	9234786	103	SRX6854753	SRS5392955	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.76341	0.34992	0.97583	0.47889	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54353	54353	SRR10126103	SRX6854752	SRS5392954	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON27 01 C12	GSM4080989		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.207435774030802	ON27 01 C12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.207435774030802	GSM4080989	GSM4080989: ON27 01 C12; Danio rerio; RNA Seq	GSM4080989	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080989	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22293_ON27_01_C12_mod.bam	bam	36635572.0	482047.0	GSM4080989 r1	0:76	A:10775220;C:6902317;G:7294618;T:11663244;N:173	76		10775220	6902317	7294618	11663244	173	SRX6854752	SRS5392954	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.6712	0.38208	0.98563	0.6672	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54354	54354	SRR10126102	SRX6854751	SRS5392953	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON28 01 D12	GSM4080988		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.361448206817182	ON28 01 D12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.361448206817182	GSM4080988	GSM4080988: ON28 01 D12; Danio rerio; RNA Seq	GSM4080988	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080988	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22294_ON28_01_D12_mod.bam	bam	48734088.0	641238.0	GSM4080988 r1	0:76	A:13468719;C:10758080;G:10910748;T:13596298;N:243	76		13468719	10758080	10910748	13596298	243	SRX6854751	SRS5392953	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.88752	0.18774	0.94911	0.46357	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54355	54355	SRR10126101	SRX6854750	SRS5392952	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON26 01 B12	GSM4080987		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.400282577622292	ON26 01 B12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.400282577622292	GSM4080987	GSM4080987: ON26 01 B12; Danio rerio; RNA Seq	GSM4080987	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080987	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22292_ON26_01_B12_mod.bam	bam	46093468.0	606493.0	GSM4080987 r1	0:76	A:12497312;C:10446137;G:10539301;T:12610508;N:210	76		12497312	10446137	10539301	12610508	210	SRX6854750	SRS5392952	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.89062	0.07593	0.95146	0.50127	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54356	54356	SRR10126100	SRX6854749	SRS5392951	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON25 01 A12	GSM4080986		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.36034551688211	ON25 01 A12	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.36034551688211	GSM4080986	GSM4080986: ON25 01 A12; Danio rerio; RNA Seq	GSM4080986	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080986	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22291_ON25_01_A12_mod.bam	bam	56456068.0	742843.0	GSM4080986 r1	0:76	A:16017845;C:12025190;G:12186747;T:16226025;N:261	76		16017845	12025190	12186747	16226025	261	SRX6854749	SRS5392951	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87174	0.20317	0.94446	0.48709	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54357	54357	SRR10126099	SRX6854748	SRS5392950	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON24 01 H11	GSM4080985		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.324713155088674	ON24 01 H11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.324713155088674	GSM4080985	GSM4080985: ON24 01 H11; Danio rerio; RNA Seq	GSM4080985	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080985	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22290_ON24_01_H11_mod.bam	bam	49961108.0	657383.0	GSM4080985 r1	0:76	A:14127615;C:10704711;G:10835971;T:14292589;N:222	76		14127615	10704711	10835971	14292589	222	SRX6854748	SRS5392950	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.87519	0.24291	0.91543	0.48833	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54358	54358	SRR10126098	SRX6854747	SRS5392949	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON20 01 D11	GSM4080984		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.345805160446015	ON20 01 D11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.345805160446015	GSM4080984	GSM4080984: ON20 01 D11; Danio rerio; RNA Seq	GSM4080984	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080984	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22286_ON20_01_D11_mod.bam	bam	45645220.0	600595.0	GSM4080984 r1	0:76	A:12652866;C:10016610;G:10144796;T:12830749;N:199	76		12652866	10016610	10144796	12830749	199	SRX6854747	SRS5392949	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8612	0.21429	0.94649	0.51433	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous System
54359	54359	SRR10126097	SRX6854746	SRS5392948	SRP221784	PRJNA565778	Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain	GSE137525	Transcriptome Analysis	Zebrafish display widespread and pronounced adult neurogenesis which is fundamental for their regeneration capability post central nervous system injury. However the cellular identity and the biological properties of adult newborn neurons are elusive for most brain areas. Here we used short term lineage tracing of radial glia progeny to prospectively isolate newborn neurons from the her4.1+ radial glia lineage in the homeostatic adult forebrain. Transcriptome analysis of radial glia newborn neurons and mature neurons using single cell sequencing identified distinct transcriptional profiles including novel markers for each population. Specifically we detected 2 separate newborn neuron types which showed diversity of cell fate commitment and location. Further analyses showed homology of these cell types to neurogenic cells in the mammalian brain identified neurogenic commitment in proliferating radial glia and indicated that glutamatergic projection neurons fate are generated in the adult zebrafish telecephalon. Thus we prospectively isolated adult newborn neurons from the adult zebrafish forebrain identified markers for newborn and mature neurons in the adult brain revealed intrinsic heterogeneity among adult newborn neurons and their homology to mammalian adult neurogenic cell types. Overall design: single cell sequencing to identify specific markers and functional subpopulations of adult newborn neurons in the zebrafish forebrain		pubmed:31908317		ON19 01 C11	GSM4080983		tissue:Brain\|sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.342848231466316	ON19 01 C11	FastQC was used to examine quality of the reads post sequencing. Alignment with GSNAP v 2017 08 15 with parameters for sample ON15 01 G10 all other samples accordingly: ‘gsnap.sse42 D /projects/seq work/user/pipeline/gmap d GRCz10 gunzip A sam t 14 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 87.ss.GRCz10.iit read group id=L22281 ON15 01 G10 read group name=ON15 01 G10 read group library=L22281 read group platform=illumina fastq/L22281 ON15 01 G10 R1.fastq.gz’ Ensembl gene annotation version 87 was used to detect exon spanning reads featureCounts v1.5.3 was used with the same Ensembl annotation to count the uniquely aligned reads to the genes and to create a counts table. Parameters: " a" "/projects/seq work/user/pipeline/annotation/danio rerio/GRCz10/EnsemblGene 87.GRCz10.TR.gtf" " s" "2" " o" "genecount/bfx811.GRCz10.e87.txt" " Q" "1" " T" "8" " tmpDir" "/tmp/418815.1.ngs.q" Genome build: GRCz10 reference inclusive the 92 ERCC Spike In transcripts Supplementary files format and content: `counts.csv` is a comma separated table and contains the raw count matrix.	Brain		adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.		sorting:MN\|FISH id:bfx811 01\|batch:bfx811\|fraction mapped:0.342848231466316	GSM4080983	GSM4080983: ON19 01 C11; Danio rerio; RNA Seq	GSM4080983	1	adult zebrafish brains were collected digested into single cells using the Papain Neural Tissue Dissociation Kit Miltenyi and sorted by FACS to isolate cells expressing GFP or mcherry The Illumina Nextera DNA library preparation kit FC 121 1031 was used to prepare libraries.	GEO Accession:GSM4080983	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP221784		intentional duplicate\|dangling references:treat as unmapped	L22285_ON19_01_C11_mod.bam	bam	44588516.0	586691.0	GSM4080983 r1	0:76	A:12252079;C:9823426;G:9954660;T:12558164;N:187	76		12252079	9823426	9954660	12558164	187	SRX6854746	SRS5392948	SRA962624	GEO	Statistical physics of living systems, Biological Physics, Max Planck Institute for the Physics of Complex Systems	1	0.8663	0.1874	0.95057	0.48221	76	B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc_generic	single_cell_generic	generic-scrnaseq-only	Germany	2019-09-16	Adult	Adult	Brain	Nervous 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");;