metadata: run_metadata: 853 rows where devstage_curation_coarse = "Larval" and tissue_curation

853 rows where devstage_curation_coarse = "Larval" and tissue_curation_coarse = "Cardiovascular System"

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.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
5879	5879	ERR1759701	ERX1826022	ERS1474296	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample2	SAMEA27136168	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27136168\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample2\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:actn2 tdEodncv44Tg\|sample name:E MTAB 5323:Sample2									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample2 s	Sample2 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz	fastq	448234901.0	6016977.0	E MTAB 5323:Sample2	0:74.50 1:0	A:118923409;C:100586009;G:99987046;T:126071553;N:2666884	74	0	118923409	100586009	99987046	126071553	2666884	ERX1826022	ERS1474296	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.88465		0.27583		0.75398		0.55917		75		B		usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5880	5880	ERR1759702	ERX1826022	ERS1474296	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample2	SAMEA27136168	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27136168\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample2\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:actn2 tdEodncv44Tg\|sample name:E MTAB 5323:Sample2									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample2 s	Sample2 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz	fastq	448116860.0	6016977.0	E MTAB 5323:Sample2 1	0:0 1:74.48	A:127811460;C:99875207;G:106561979;T:113792335;N:75879	0	74	127811460	99875207	106561979	113792335	75879	ERX1826022	ERS1474296	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.91589		0.2509		0.79005		0.54852		75		B		usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5881	5881	ERR1759699	ERX1826021	ERS1474295	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample1	SAMEA27135418	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27135418\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample1\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:Nls mCherryncv11Tg\|sample name:E MTAB 5323:Sample1									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample1 s	Sample1 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz	fastq	766363334.0	10284347.0	E MTAB 5323:Sample1	0:74.52 1:0	A:201960096;C:174999154;G:173403690;T:211341998;N:4658396	74	0	201960096	174999154	173403690	211341998	4658396	ERX1826021	ERS1474295	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.86003		0.20554		0.76301		0.55753		74		B		usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
5882	5882	ERR1759700	ERX1826021	ERS1474295	ERP020578	PRJEB18632	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E-MTAB-5323	Transcriptome Analysis	The aim of this analysis is to uncover novel molecules synthesized and secreted from cardiomyocytes.	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2016 12 15\|ArrayExpress:E MTAB 5323		Protocols: To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Sample1	SAMEA27135418	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute	ENA first public:2016 12 20\|ENA last update:2016 12 15\|External Id:SAMEA27135418\|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|INSDC first public:2016 12 20T17:02:09Z\|INSDC last update:2016 12 15T11:23:10Z\|INSDC status:public\|Submitter Id:E MTAB 5323:Sample1\|broker name:ArrayExpress\|cell type:cardiac myocyte\|common name:zebrafish\|developmental stage:72 hpf\|genotype:Tgmyl7:Nls mCherryncv11Tg\|sample name:E MTAB 5323:Sample1									Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	E MTAB 5323:Sample1 s	Sample1 s	RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	To obtain only cardiomyocytes from the heart two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture’s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently the sample was end repaired dA tailed adaptor ligated and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.	Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	Illumina MiSeq	ERP020578	Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf	ENA FIRST PUBLIC:2016 12 20\|ENA LAST UPDATE:2018 11 16	mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz	fastq	766251339.0	10284347.0	E MTAB 5323:Sample1 1	0:0 1:74.51	A:214234414;C:174215653;G:180382062;T:197361982;N:57228	0	74	214234414	174215653	180382062	197361982	57228	ERX1826021	ERS1474295	ERA776061	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute\|European Nucleotide Archive	1	0.87766		0.21561		0.77477		0.53919		73		B		usable mapping rate	illumina	miseq	full_length	poly_a	nebnext	bulk	unknown	unknown	Japan	2016-12-15	Larval	Larval	Heart	Cardiovascular System
10216	10216	ERR6501834	ERX6129007	ERS7415871	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Uninjured 3	SAMEA9691614	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691614\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Uninjured 3\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 6 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Uninjured 3\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Uninjured 3 p	Uninjured 3 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz	fastq fastq	18723567013.0	65061888.0	E MTAB 10860:un 3 R	0:143.87 1:143.91	A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225	143	143	4417527025	4932613578	4960694819	4412305366	426225	ERX6129007	ERS7415871	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.96755	0.96744	0.18873	0.18936	0.72868	0.73235	0.632	0.6437	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
10217	10217	ERR6501833	ERX6129006	ERS7415870	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Uninjured 2	SAMEA9691613	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691613\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Uninjured 2\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 5 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Uninjured 2\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Uninjured 2 p	Uninjured 2 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz	fastq fastq	16871358399.0	59064661.0	E MTAB 10860:un 2 R	0:142.77 1:142.88	A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056	142	142	4041490134	4380856328	4414614946	4033723935	673056	ERX6129006	ERS7415870	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.96589	0.9656	0.15519	0.15447	0.70887	0.71062	0.60267	0.60735	150	147	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
10218	10218	ERR6501832	ERX6129005	ERS7415869	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Uninjured 1	SAMEA9691612	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691612\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Uninjured 1\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 4 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Uninjured 1\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Uninjured 1 p	Uninjured 1 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz	fastq fastq	22029484310.0	76938931.0	E MTAB 10860:un 1 R	0:143.11 1:143.22	A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752	143	143	5407867825	5589867496	5636111894	5394805343	831752	ERX6129005	ERS7415869	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.9602	0.95957	0.14282	0.14408	0.69649	0.69954	0.56712	0.56916	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
10219	10219	ERR6501831	ERX6129004	ERS7415868	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Injured 3	SAMEA9691611	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691611\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Injured 3\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 3 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Injured 3\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Injured 3 p	Injured 3 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:laser injury	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz	fastq fastq	7393087749.0	25640713.0	E MTAB 10860:in 3 R	0:144.14 1:144.20	A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175	144	144	1776335117	1913125420	1928181998	1775255039	190175	ERX6129004	ERS7415868	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.96032	0.96001	0.15921	0.15882	0.71417	0.71869	0.59876	0.595	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
10220	10220	ERR6501830	ERX6129003	ERS7415867	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Injured 2	SAMEA9691610	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691610\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Injured 2\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 2 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Injured 2\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Injured 2 p	Injured 2 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:laser injury	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz	fastq fastq	9437508186.0	33059234.0	E MTAB 10860:in 2 R	0:142.70 1:142.77	A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351	142	142	2291798254	2421252733	2436117818	2288107030	232351	ERX6129003	ERS7415867	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.96099	0.96042	0.14616	0.14802	0.70331	0.70674	0.53288	0.54459	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
10221	10221	ERR6501829	ERX6129002	ERS7415866	ERP131229	PRJEB46994	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E-MTAB-10860	Transcriptome Analysis	This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01		Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Injured 1	SAMEA9691609	University Of Edinburgh	ENA first public:2021 10 01\|ENA last update:2021 10 01\|External Id:SAMEA9691609\|INSDC center alias:UOE\|INSDC center name:University Of Edinburgh\|INSDC first public:2021 10 01T00:25:01Z\|INSDC last update:2021 10 01T00:25:01Z\|INSDC status:public\|Submitter Id:E MTAB 10860:Injured 1\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:pool 1 of 200 larvae\|organism part:heart\|sample name:E MTAB 10860:Injured 1\|sex:not available\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	E MTAB 10860:Injured 1 p	Injured 1 p	Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf	Experimental Factor: injury:laser injury	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	ERP131229	Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf	ENA FIRST PUBLIC:2021 10 01\|ENA LAST UPDATE:2021 10 01	in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz	fastq fastq	15465552702.0	54194727.0	E MTAB 10860:in 1 R	0:142.59 1:142.78	A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648	142	142	3807777989	3911855097	3946385823	3798685145	848648	ERX6129002	ERS7415866	ERA5680505	University Of Edinburgh\|European Nucleotide Archive	University Of Edinburgh\|European Nucleotide Archive	2	0.95721	0.95688	0.14331	0.14374	0.70262	0.70445	0.5114	0.52855	140	140	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United Kingdom	2021-10-01	Larval	Larval	Heart	Cardiovascular System
26482	26482	SRR25930974	SRX21649989	SRS18818461	SRP458853	PRJNA1013567	scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts	GSE242483	Transcriptome Analysis	Seeking to identify additional transcription factors required for cardiac valve formation we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established and at 80 hpf when forming valves are first observed		pubmed:38748804		80hpf	GSM7764482		source name:heart\|tissue:heart\|genotype:wild type\|age:80hpf\|geo loc name:missing\|collection date:missing	80hpf	Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding and cell clustering were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs	heart		Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000		tissue:heart\|genotype:wild type\|age:80hpf	GSM7764482	GSM7764482: 80hpf; Danio rerio; RNA Seq	GSM7764482 r1	GSM7764482	1	Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3 1 10xGenomics. scRNA seq library preparation was done using a standard protocol and sequencing was done on a Nextseq2000		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP458853			Giulia_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz	fastq fastq	18811433188.0	225273324.0	GSM7764482 r1	0:28 1:55.50	A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878	28	55	5135587480	4020079745	4129712330	5427444755	98608878	SRX21649989	SRS18818461	SRA1706674	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	Bioinformatics, Max-Planck-Institute for Heart and Lung Research	2	0.00187	0.93611	0.00071	0.16105	0.99626	0.79825	0.41545	0.50249	28	55	T	B	sc-like readlen	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2023-09-06	Larval	Larval	Heart	Cardiovascular System
28771	28771	SRR26639098	SRX22339478	SRS19389127	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 2 snRNAseq	GSM7880035		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880035	GSM7880035: sibling replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880035 r1	GSM7880035	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_2_S1_L001_R1_001.fastq.gz sib_2_S1_L001_R2_001.fastq.gz	fastq fastq	29585942468.0	250728326.0	GSM7880035 r1	0:29 1:89	A:8869085825;C:6519678188;G:6681924988;T:7515095066;N:158401	29	89	8869085825	6519678188	6681924988	7515095066	158401	SRX22339478	SRS19389127	SRA1744308	University of Bern	University of Bern	2	0.03708	0.89742	0.02638	0.33817	0.98766	0.87265	0.50529	0.84547	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28772	28772	SRR26639099	SRX22339478	SRS19389127	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 2 snRNAseq	GSM7880035		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880035	GSM7880035: sibling replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880035 r1	GSM7880035	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz	fastq fastq	29238445684.0	247783438.0	GSM7880035 r2	0:29 1:89	A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758	29	89	8764474921	6441070570	6601843083	7430828352	228758	SRX22339478	SRS19389127	SRA1744308	University of Bern	University of Bern	2	0.03758	0.89628	0.02664	0.33912	0.98711	0.87442	0.4887	0.42456	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28773	28773	SRR26639100	SRX22339477	SRS19389126	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 1 snRNAseq	GSM7880034		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880034	GSM7880034: sibling replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880034 r1	GSM7880034	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_1_S1_L001_R1_001.fastq.gz sib_1_S1_L001_R2_001.fastq.gz	fastq fastq	24652163520.0	208916640.0	GSM7880034 r1	0:29 1:89	A:7206225437;C:5487875216;G:5870141423;T:6087790451;N:130993	29	89	7206225437	5487875216	5870141423	6087790451	130993	SRX22339477	SRS19389126	SRA1744308	University of Bern	University of Bern	2	0.04136	0.8662	0.02868	0.3899	0.98597	0.86906	0.42284	0.79265	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28774	28774	SRR26639101	SRX22339477	SRS19389126	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		sibling replicate 1 snRNAseq	GSM7880034		source name:heart\|tissue:heart\|age:3dpf\|genotype:wt sibling\|geo loc name:missing\|collection date:missing	sibling replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:wt sibling	GSM7880034	GSM7880034: sibling replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880034 r1	GSM7880034	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	sib_1_S1_L002_R1_001.fastq.gz sib_1_S1_L002_R2_001.fastq.gz	fastq fastq	24333156656.0	206213192.0	GSM7880034 r2	0:29 1:89	A:7112369699;C:5414867956;G:5792728480;T:6013000607;N:189914	29	89	7112369699	5414867956	5792728480	6013000607	189914	SRX22339477	SRS19389126	SRA1744308	University of Bern	University of Bern	2	0.04141	0.86578	0.02866	0.39157	0.98614	0.8704	0.42701	0.78792	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28775	28775	SRR26639102	SRX22339476	SRS19389125	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 2 snRNAseq	GSM7880033		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880033	GSM7880033: spns mutant replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880033 r1	GSM7880033	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_2_S1_L001_R1_001.fastq.gz mut_2_S1_L001_R2_001.fastq.gz	fastq fastq	33067082062.0	280229509.0	GSM7880033 r1	0:29 1:89	A:9837791085;C:7302189072;G:7479072379;T:8447851569;N:177957	29	89	9837791085	7302189072	7479072379	8447851569	177957	SRX22339476	SRS19389125	SRA1744308	University of Bern	University of Bern	2	0.03975	0.89392	0.02827	0.35098	0.98693	0.87572	0.42665	0.8308	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28776	28776	SRR26639103	SRX22339476	SRS19389125	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 2 snRNAseq	GSM7880033		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 2 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880033	GSM7880033: spns mutant replicate 2 snRNAseq; Danio rerio; RNA Seq	GSM7880033 r1	GSM7880033	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_2_S1_L002_R1_001.fastq.gz mut_2_S1_L002_R2_001.fastq.gz	fastq fastq	32794778418.0	277921851.0	GSM7880033 r2	0:29 1:89	A:9757463504;C:7238976466;G:7415128557;T:8382951671;N:258220	29	89	9757463504	7238976466	7415128557	8382951671	258220	SRX22339476	SRS19389125	SRA1744308	University of Bern	University of Bern	2	0.04055	0.89543	0.02892	0.35129	0.98654	0.87655	0.45394	0.85056	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28777	28777	SRR26639104	SRX22339475	SRS19389124	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 1 snRNAseq	GSM7880032		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880032	GSM7880032: spns mutant replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880032 r1	GSM7880032	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz	fastq fastq	30027997254.0	254474553.0	GSM7880032 r1	0:29 1:89	A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572	29	89	9128230353	6473885422	6895366272	7530354635	160572	SRX22339475	SRS19389124	SRA1744308	University of Bern	University of Bern	2	0.03908	0.86231	0.0274	0.38263	0.98701	0.87113	0.48114	0.78783	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
28778	28778	SRR26639105	SRX22339475	SRS19389124	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissect…		pubmed:39720516		spns mutant replicate 1 snRNAseq	GSM7880032		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and d…		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880032	GSM7880032: spns mutant replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880032 r1	GSM7880032	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired …		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP469857		loader:fastq load.py	mut_1_S1_L002_R1_001.fastq.gz mut_1_S1_L002_R2_001.fastq.gz	fastq fastq	29506651188.0	250056366.0	GSM7880032 r2	0:29 1:89	A:8967217701;C:6359649244;G:6775979696;T:7403576105;N:228442	29	89	8967217701	6359649244	6775979696	7403576105	228442	SRX22339475	SRS19389124	SRA1744308	University of Bern	University of Bern	2	0.03885	0.86188	0.02749	0.38666	0.98644	0.86975	0.46306	0.79451	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System
29086	29086	SRR27015250	SRX22707800	SRS19700101	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3	GSM7927521		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927521	GSM7927521: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 3; Danio rerio; RNA Seq	GSM7927521 r1	GSM7927521	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz	fastq	1709509823.0	28403358.0	GSM7927521 r1	0:60.19	A:400293032;C:330429588;G:326652799;T:383291002;N:268843402	60		400293032	330429588	326652799	383291002	268843402	SRX22707800	SRS19700101	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90079		0.0827		0.81406		0.64557		35		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29087	29087	SRR27015251	SRX22707799	SRS19700100	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2	GSM7927520		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927520	GSM7927520: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 2; Danio rerio; RNA Seq	GSM7927520 r1	GSM7927520	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz	fastq	1740891025.0	28211981.0	GSM7927520 r1	0:61.71	A:419094150;C:347792831;G:345450108;T:407537501;N:221016435	61		419094150	347792831	345450108	407537501	221016435	SRX22707799	SRS19700100	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90091		0.13293		0.78464		0.54281		69		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29088	29088	SRR27015252	SRX22707798	SRS19700099	SRP475323	PRJNA1047551	Identification of genes important during atrial myocardial morphogenesis	GSE249149	Transcriptome Analysis	Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures. We aimed to identify the genes involved during this process and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.		pubmed:39289341		Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1	GSM7927519		source name:embryonic heart\|tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf loc name:missing\|collection date:missing	Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1	Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al. STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format multi mapping ribosomal or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix	embryonic heart		miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		tissue:embryonic heart\|cell type:cardiomyocyte\|genotype:wild type\|treatment:72 hpf	GSM7927519	GSM7927519: Wild type zebrafish atrial cardiomyocytes 72 hpf rep 1; Danio rerio; RNA Seq	GSM7927519 r1	GSM7927519	1	miRNeasy micro Kit Qiagen using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	SRP475323		loader:fastq load.py	dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz	fastq	1930552948.0	30996774.0	GSM7927519 r1	0:62.28	A:468769814;C:389869994;G:387622687;T:454801262;N:229489191	62		468769814	389869994	387622687	454801262	229489191	SRX22707798	SRS19700099	SRA1761360	MPI for heart and lung research	MPI for heart and lung research	1	0.90465		0.10656		0.79586		0.55674		72		B		usable mapping rate	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2023-12-01	Larval	Larval	Heart	Cardiovascular System
29569	29569	SRR27368685	SRX23045203	SRS20006222	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg6 Non cardiomyocytes	GSM7995233		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg6 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995233	GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995233 r1	GSM7995233	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg6_S42_L008_R1_001.fastq.gz	fastq	527477356.0	10449387.0	GSM7995233 r1	0:50.48	A:141759410;C:113279303;G:116384028;T:155860577;N:194038	50		141759410	113279303	116384028	155860577	194038	SRX23045203	SRS20006222	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.79175		0.2711		0.7587		0.61924		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29570	29570	SRR27368686	SRX23045202	SRS20006221	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg5 Non cardiomyocytes	GSM7995232		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg5 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995232	GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995232 r1	GSM7995232	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg5_S41_L008_R1_001.fastq.gz	fastq	3356204764.0	66511806.0	GSM7995232 r1	0:50.46	A:860342578;C:766593257;G:774473426;T:953992775;N:802728	50		860342578	766593257	774473426	953992775	802728	SRX23045202	SRS20006221	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.70469		0.23332		0.76992		0.62712		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29571	29571	SRR27368687	SRX23045201	SRS20006220	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			500kGFPneg4 Non cardiomyocytes	GSM7995231		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control\|geo loc name:missing\|collection date:missing	500kGFPneg4 Non cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Non cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPneg\|treatment:Control	GSM7995231	GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq	GSM7995231 r1	GSM7995231	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			500kGFPneg4_S40_L008_R1_001.fastq.gz	fastq	3075367681.0	60986692.0	GSM7995231 r1	0:50.43	A:807059039;C:682279458;G:696326840;T:888937765;N:764579	50		807059039	682279458	696326840	888937765	764579	SRX23045201	SRS20006220	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.74255		0.26699		0.76786		0.63053		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29572	29572	SRR27368688	SRX23045200	SRS20006219	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos3 Cardiomyocytes	GSM7995230		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos3 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995230	GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995230 r1	GSM7995230	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos3_S39_L008_R1_001.fastq.gz	fastq	2938808771.0	58361915.0	GSM7995230 r1	0:50.35	A:533261626;C:883704329;G:825929620;T:694986734;N:926462	50		533261626	883704329	825929620	694986734	926462	SRX23045200	SRS20006219	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.12924		0.05415		0.92034		0.70896		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29573	29573	SRR27368689	SRX23045199	SRS20006218	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos2 Cardiomyocytes	GSM7995229		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos2 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995229	GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995229 r1	GSM7995229	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos2_S38_L008_R1_001.fastq.gz	fastq	3006409096.0	59645543.0	GSM7995229 r1	0:50.40	A:560839480;C:885691877;G:830121593;T:728932219;N:823927	50		560839480	885691877	830121593	728932219	823927	SRX23045199	SRS20006218	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.17805		0.06115		0.89769		0.68731		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
29574	29574	SRR27368690	SRX23045198	SRS20006217	SRP480346	PRJNA1057908	An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]	GSE252151	Transcriptome Analysis	cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types predominantly cardiomyocytes. Therefore cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development as they share a number of physiological features with the human heart during development. Therefore we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes validating these genomic regions as cardiac regulatory elements. We share this comprehensive reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells n=3 biological replicates and GFP negative cells 500 000 cells n=3 biological replicates were collected and RNA sequencing was performed on these samples.	parent bioproject:PRJNA1057890			30kGFPpos1 Cardiomyocytes	GSM7995228		source name:Heart\|tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control\|geo loc name:missing\|collection date:missing	30kGFPpos1 Cardiomyocytes	FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin 2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al 2018 using default parameters. There were two sets of counts obtained the first were the reads mapped to genome Zv9 and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9 Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample	Heart		RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:Heart\|cell line:Primary cells\|cell type:Cardiomyocytes\|genotype:Tgmyl7::GFP\|gfp status:GFPpos\|treatment:Control	GSM7995228	GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq	GSM7995228 r1	GSM7995228	1	RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866 Qubit™ RNA HS Assay Kit Q32852 ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 3000	SRP480346			30kGFPpos1_S37_L008_R1_001.fastq.gz	fastq	3254639839.0	64665631.0	GSM7995228 r1	0:50.33	A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592	50		545193535	1023804678	938318027	746302007	1021592	SRX23045198	SRS20006217	SRA1776396	Australian Regenerative Medicine Institute, Monash University	Australian Regenerative Medicine Institute, Monash University	1	0.05453		0.01921		0.9643		0.78064		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2023-12-27	Undetermined	Larval	Heart	Cardiovascular System
30708	30708	SRR28329751	SRX23938186	SRS20741667	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DAPT 3	GSM8144970		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT\|geo loc name:missing\|collection date:missing	DAPT 3	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT	GSM8144970	GSM8144970: DAPT 3; Danio rerio; RNA Seq	GSM8144970 r1	GSM8144970	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DAPT_3_1.fq.gz DAPT_3_2.fq.gz	fastq fastq	6899234400.0	34496172.0	GSM8144970 r1	0:100 1:100	A:1864675679;C:1564709308;G:1588106892;T:1881742521;N:0	100	100	1864675679	1564709308	1588106892	1881742521	0	SRX23938186	SRS20741667	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.93368	0.93504	0.09899	0.09916	0.67174	0.67095	0.51572	0.5101	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30709	30709	SRR28329752	SRX23938185	SRS20741666	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DAPT 2	GSM8144969		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT\|geo loc name:missing\|collection date:missing	DAPT 2	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT	GSM8144969	GSM8144969: DAPT 2; Danio rerio; RNA Seq	GSM8144969 r1	GSM8144969	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DAPT_2_1.fq.gz DAPT_2_2.fq.gz	fastq fastq	6920695600.0	34603478.0	GSM8144969 r1	0:100 1:100	A:1880782056;C:1560368169;G:1581248339;T:1898297036;N:0	100	100	1880782056	1560368169	1581248339	1898297036	0	SRX23938185	SRS20741666	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.93355	0.93357	0.10276	0.10282	0.67363	0.67361	0.51703	0.52041	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30710	30710	SRR28329753	SRX23938184	SRS20741665	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DAPT 1	GSM8144968		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT\|geo loc name:missing\|collection date:missing	DAPT 1	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DAPT	GSM8144968	GSM8144968: DAPT 1; Danio rerio; RNA Seq	GSM8144968 r1	GSM8144968	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DAPT_1_1.fq.gz DAPT_1_2.fq.gz	fastq fastq	6917244000.0	34586220.0	GSM8144968 r1	0:100 1:100	A:1871550461;C:1566067610;G:1585361217;T:1894264712;N:0	100	100	1871550461	1566067610	1585361217	1894264712	0	SRX23938184	SRS20741665	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.9357	0.93705	0.09751	0.09758	0.67387	0.67363	0.51842	0.51997	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30711	30711	SRR28329754	SRX23938183	SRS20741664	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DMSO 3	GSM8144967		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO\|geo loc name:missing\|collection date:missing	DMSO 3	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO	GSM8144967	GSM8144967: DMSO 3; Danio rerio; RNA Seq	GSM8144967 r1	GSM8144967	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DMSO_3_2.fq.gz DMSO_3_1.fq.gz	fastq fastq	6919708800.0	34598544.0	GSM8144967 r1	0:100 1:100	A:1894083722;C:1545002324;G:1569342322;T:1911280432;N:0	100	100	1894083722	1545002324	1569342322	1911280432	0	SRX23938183	SRS20741664	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.93873	0.93836	0.10256	0.10261	0.66068	0.6616	0.52724	0.52601	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30712	30712	SRR28329755	SRX23938182	SRS20741663	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DMSO 2	GSM8144966		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO\|geo loc name:missing\|collection date:missing	DMSO 2	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO	GSM8144966	GSM8144966: DMSO 2; Danio rerio; RNA Seq	GSM8144966 r1	GSM8144966	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DMSO_2_1.fq.gz DMSO_2_2.fq.gz	fastq fastq	6902487800.0	34512439.0	GSM8144966 r1	0:100 1:100	A:1892099736;C:1540950565;G:1559704613;T:1909732886;N:0	100	100	1892099736	1540950565	1559704613	1909732886	0	SRX23938182	SRS20741663	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.93535	0.93511	0.10112	0.10162	0.66541	0.66592	0.51543	0.51644	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30713	30713	SRR28329756	SRX23938181	SRS20741662	SRP494974	PRJNA1087264	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression	GSE261479	Transcriptome Analysis	Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods: Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 µM were collected for RNA seq.		pubmed:40053597		DMSO 1	GSM8144965		source name:hearts\|tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO\|geo loc name:missing\|collection date:missing	DMSO 1	Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo gene counts of each slice were merged into a count matrix and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix between treatment samples and wild type samples.	hearts	60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 μM to 96 hpf.	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols	Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h.	tissue:hearts\|strain:Tgmyl7:mCherry\|age:96 hpf\|treatment:DMSO	GSM8144965	GSM8144965: DMSO 1; Danio rerio; RNA Seq	GSM8144965 r1	GSM8144965	1	1 μg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP494974			DMSO_1_1.fq.gz DMSO_1_2.fq.gz	fastq fastq	6918299800.0	34591499.0	GSM8144965 r1	0:100 1:100	A:1887082093;C:1551476280;G:1575428027;T:1904313400;N:0	100	100	1887082093	1551476280	1575428027	1904313400	0	SRX23938181	SRS20741662	SRA1823438	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.93809	0.93843	0.098	0.09793	0.66647	0.66709	0.53463	0.52582	100	100	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2024-03-13	Larval	Larval	Heart	Cardiovascular System
30775	30775	SRR28357669	SRX23962905	SRS20762620	SRP495490	PRJNA1088483	Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA Seq]	GSE261718	Other	Purpose: To explore the endogenous expression pattern of Erbb2. Methods: Approximately 1000 hearts dissected from 72 hpf Tgmyl7:mCherry embryos were digested in 0.25% trypsin EDTA solution for single cell RNA sequencing. Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2 but weakly expressed in subcluster 3 10 and 12. Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation. Overall design: 72 hpf Tgmyl7:mCherry zebrafish hearts were collected for single cell RNA sequencing.		pubmed:40053597		S72hpf trunks	GSM8149579		source name:zebrafish hearts\|tissue:zebrafish hearts\|cell line:Tgmyl7:mCherry heart cells\|cell type:zebrafish heart cells\|geo loc name:missing\|collection date:missing	S72hpf trunks	Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: zip compressed files include filtered gene bc matrices post running CellRanger pipeline	zebrafish hearts		A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer’s instructions. Single cell RNA Seq 10x	Dechorionated zebrafish embryos were maintained in 0.3x Danieau’s Buffer at 28 °C with a photoperiod of 14/10 h light/dark.	tissue:zebrafish hearts\|cell line:Tgmyl7:mCherry heart cells\|cell type:zebrafish heart cells	GSM8149579	GSM8149579: S72hpf trunks; Danio rerio; RNA Seq	GSM8149579 r1	GSM8149579	1	A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 °C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer's instructions. Single cell RNA Seq 10x		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP495490			zebrafish_heart_72h_R1_fastq.gz zebrafish_heart_72h_R2_fastq.gz	fastq fastq	155978889600.0	519929632.0	GSM8149579 r1	0:150 1:150	A:63302225780;C:28042347630;G:26792086978;T:37838422350;N:3806862	150	150	63302225780	28042347630	26792086978	37838422350	3806862	SRX23962905	SRS20762620	SRA1825277	Institute of genetics, Zhejiang University	Institute of genetics, Zhejiang University	2	0.0	0.92044	0.0	0.11022	1.0	0.80996		0.54499	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2024-03-15	Larval	Larval	Heart	Cardiovascular System
32610	32610	SRR29325926	SRX24842083	SRS21553258	SRP512516	PRJNA1121299	Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study "The heart is a niche for hematopoietic stem and progenitor cells in zebrafish."	GSE269378	Transcriptome Analysis	We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study we uncovered the presence of an endocardial hematopoietic cluster along with other significant clusters including valve endocardial and interstitial cells and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells and further analyzed using scRNAseq.		pubmed:39217144		EC HC 3d	GSM8314111		source name:Heart\|tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:72 hpf loc name:missing\|collection date:missing	EC HC 3d	Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding McInnes & Healy https://arxiv.org/abs/1802.03426 and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs	Heart		Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Ne…	Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf	tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:72 hpf	GSM8314111	GSM8314111: EC HC 3d; Danio rerio; RNA Seq	GSM8314111 r1	GSM8314111	1	Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Ne…		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000	SRP512516			Felix_10x_Lib_EC-HC_3d_R1.fastq.gz Felix_10x_Lib_EC-HC_3d_R2.fastq.gz	fastq fastq	34745112542.0	437132766.0	GSM8314111 r1	0:28 1:51.48	A:9310358713;C:7641472951;G:8108829079;T:9501691105;N:182760694	28	51	9310358713	7641472951	8108829079	9501691105	182760694	SRX24842083	SRS21553258	SRA1892449	MPI for heart and lung research	MPI for heart and lung research												T	B	sc-like readlen	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Germany	2024-06-07	Larval	Larval	Heart	Cardiovascular System
33934	33934	SRR30947094	SRX26349630	SRS22874784	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1+/+ wild type replicate #3	GSM8565205		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565205	GSM8565205: whole heart tak1+/+ wild type replicate #3; Danio rerio; RNA Seq	GSM8565205 r1	GSM8565205	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	4449566200.0	22247831.0	GSM8565205 r1	0:100 1:100	A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0	100	100	1179341017	1046638560	1046356098	1177230525	0	SRX26349630	SRS22874784	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33935	33935	SRR30947095	SRX26349629	SRS22874783	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1+/+ wild type replicate #2	GSM8565204		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565204	GSM8565204: whole heart tak1+/+ wild type replicate #2; Danio rerio; RNA Seq	GSM8565204 r1	GSM8565204	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			WT_2_1.fq.gz WT_2_2.fq.gz	fastq fastq	4519627600.0	22598138.0	GSM8565204 r1	0:100 1:100	A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0	100	100	1207344552	1055139553	1056806709	1200336786	0	SRX26349629	SRS22874783	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33936	33936	SRR30947096	SRX26349628	SRS22874781	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1+/+ wild type replicate #1	GSM8565203		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565203	GSM8565203: whole heart tak1+/+ wild type replicate #1; Danio rerio; RNA Seq	GSM8565203 r1	GSM8565203	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	4496601200.0	22483006.0	GSM8565203 r1	0:100 1:100	A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0	100	100	1201390946	1050348674	1051355386	1193506194	0	SRX26349628	SRS22874781	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33937	33937	SRR30947097	SRX26349627	SRS22874780	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1 / mutant replicate #3	GSM8565202		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565202	GSM8565202: whole heart tak1 / mutant replicate #3; Danio rerio; RNA Seq	GSM8565202 r1	GSM8565202	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			mut_3_1.fq.gz mut_3_2.fq.gz	fastq fastq	4451759600.0	22258798.0	GSM8565202 r1	0:100 1:100	A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0	100	100	1167798041	1064608876	1066460994	1152891689	0	SRX26349627	SRS22874780	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33938	33938	SRR30947098	SRX26349626	SRS22874782	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1 / mutant replicate #2	GSM8565201		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565201	GSM8565201: whole heart tak1 / mutant replicate #2; Danio rerio; RNA Seq	GSM8565201 r1	GSM8565201	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			mut_2_1.fq.gz mut_2_2.fq.gz	fastq fastq	4534495200.0	22672476.0	GSM8565201 r1										SRX26349626	SRS22874782	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33939	33939	SRR30947099	SRX26349625	SRS22874779	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…				whole heart tak1 / mutant replicate #1	GSM8565200		source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf		RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565200	GSM8565200: whole heart tak1 / mutant replicate #1; Danio rerio; RNA Seq	GSM8565200 r1	GSM8565200	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826			mut_1_1.fq.gz mut_1_2.fq.gz	fastq fastq	4425052600.0	22125263.0	GSM8565200 r1	0:100 1:100	A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0	100	100	1161989932	1055452567	1055912540	1151697561	0	SRX26349625	SRS22874779	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
40968	40968	SRR3498282	SRX1756828	SRS1433359	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		6dpf E1	GSM2150746		source name:Endothelial cell\|developmental stage:6 dpf\|tissue:Endothelial\|stain:GFP	6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6 dpf\|tissue:Endothelial\|stain:GFP	GSM2150746	GSM2150746: 6dpf E1; Danio rerio; RNA Seq	GSM2150746		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150746	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847			EF_036_004_TGACCA_L002_R1.fastq.gz	fastq	446212036.0	5871211.0	GSM2150746 r1	0:76	A:121356950;C:99664887;G:97289960;T:122019647;N:5880592	76		121356950	99664887	97289960	122019647	5880592	SRX1756828	SRS1433359	SRA424807	GEO	Internal Medicine, Yale University	1	0.76652		0.13082		0.73985		0.47925		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40969	40969	SRR3498281	SRX1756827	SRS1433358	SRP074847	PRJNA321312	mRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81335	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		72hpf E1	GSM2150745		source name:Endothelial cell\|developmental stage:72 hpf\|tissue:Endothelial\|stain:GFP	72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include FPKM values for each Sample .	Endothelial cell		Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72 hpf\|tissue:Endothelial\|stain:GFP	GSM2150745	GSM2150745: 72hpf E1; Danio rerio; RNA Seq	GSM2150745		1	Transgenic fish were treated with Liberase to dissociate the cells. post FACS sorting the GFP positive RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150745	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074847			EF_035_003_TTAGGC_L002_R1.fastq.gz	fastq	533039908.0	7013683.0	GSM2150745 r1	0:76	A:141643030;C:119112106;G:118099940;T:147160011;N:7024821	76		141643030	119112106	118099940	147160011	7024821	SRX1756827	SRS1433358	SRA424807	GEO	Internal Medicine, Yale University	1	0.86605		0.1329		0.72253		0.49856		76		B		usable mapping rate	illumina	early_illumina	unknown	small_rna	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40972	40972	SRR3498294	SRX1756840	SRS1433371	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 72hpf E2	GSM2150819		source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150819	GSM2150819: NoEndo 72hpf E2; Danio rerio; miRNA Seq	GSM2150819		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150819	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			NoEndo_72hpf_E2.fastq.gz	fastq	797509876.0	10493551.0	GSM2150819 r1	0:76	A:182564842;C:199547592;G:199064466;T:216287390;N:45586	76		182564842	199547592	199064466	216287390	45586	SRX1756840	SRS1433371	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40973	40973	SRR3498293	SRX1756839	SRS1433370	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 72hpf E1	GSM2150818		source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	NoEndo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150818	GSM2150818: NoEndo 72hpf E1; Danio rerio; miRNA Seq	GSM2150818		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150818	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			NoEndo_72hpf_E1.fastq.gz	fastq	1864172232.0	24528582.0	GSM2150818 r1	0:76	A:426671762;C:469538477;G:458132395;T:509711525;N:118073	76		426671762	469538477	458132395	509711525	118073	SRX1756839	SRS1433370	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40974	40974	SRR3498292	SRX1756838	SRS1433369	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		NoEndo 6dpf E1	GSM2150817		source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	NoEndo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150817	GSM2150817: NoEndo 6dpf E1; Danio rerio; miRNA Seq	GSM2150817		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150817	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			NoEndo_6dpf_E1.fastq.gz	fastq	1414849364.0	18616439.0	GSM2150817 r1	0:76	A:315250036;C:366906308;G:364673112;T:367938758;N:81150	76		315250036	366906308	364673112	367938758	81150	SRX1756838	SRS1433369	SRA424808	GEO	Internal Medicine, Yale University	1	1e-05		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40978	40978	SRR3498288	SRX1756834	SRS1433365	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 72hpf E2	GSM2150813		source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150813	GSM2150813: Endo 72hpf E2; Danio rerio; miRNA Seq	GSM2150813		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150813	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			Endo_72hpf_E2.fastq.gz	fastq	438128980.0	5764855.0	GSM2150813 r1	0:76	A:101851745;C:114159902;G:115733669;T:106360221;N:23443	76		101851745	114159902	115733669	106360221	23443	SRX1756834	SRS1433365	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05		1e-05		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40979	40979	SRR3498287	SRX1756833	SRS1433364	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 72hpf E1	GSM2150812		source name:Endothelial cell\|developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	Endo 72hpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:72hpf\|tissue:Endothelial\|stain:GFP	GSM2150812	GSM2150812: Endo 72hpf E1; Danio rerio; miRNA Seq	GSM2150812		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150812	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			Endo_72hpf_E1.fastq.gz	fastq	1267915068.0	16683093.0	GSM2150812 r1	0:76	A:321606522;C:310505837;G:323829249;T:311892892;N:80568	76		321606522	310505837	323829249	311892892	80568	SRX1756833	SRS1433364	SRA424808	GEO	Internal Medicine, Yale University	1	0.0		0.0		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
40980	40980	SRR3498286	SRX1756832	SRS1433363	SRP074848	PRJNA321321	microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues	GSE81340	Transcriptome Analysis	Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate	parent bioproject:PRJNA321317	pubmed:28350988;pubmed:33273096		Endo 6dpf E1	GSM2150811		source name:Endothelial cell\|developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	Endo 6dpf E1	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	Endothelial cell		Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.	developmental stage:6dpf\|tissue:Endothelial\|stain:GFP	GSM2150811	GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq	GSM2150811		1	Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2150811	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer	SRP074848			Endo_6dpf_E1.fastq.gz	fastq	890474824.0	11716774.0	GSM2150811 r1	0:76	A:230419087;C:212029155;G:232306960;T:215672618;N:47004	76		230419087	212029155	232306960	215672618	47004	SRX1756832	SRS1433363	SRA424808	GEO	Internal Medicine, Yale University	1	2e-05		1e-05		1.0				76		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	United States	2016-05-11	Larval	Larval	Endothelium	Cardiovascular System
41259	41259	SRR4017369	SRX2011203	SRS1608491	SRP081209	PRJNA338400	Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq	GSE85416	Transcriptome Analysis	We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues		pubmed:28455512		embryonic heart 1	GSM2266456		source name:zebrafish embryonic heart\|developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	embryonic heart 1	The flow cells were sequenced as 50×2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9	zebrafish embryonic heart		Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	GSM2266456	GSM2266456: embryonic heart 1; Danio rerio; RNA Seq	GSM2266456		1	Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2266456	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP081209			4dpf_embryonic_heart-4.FCD29WDACXX_L8_ITTAGGC.bam.R1.fastq.gz 4dpf_embryonic_heart-4.FCD29WDACXX_L8_ITTAGGC.bam.R2.fastq.gz	fastq fastq	4434115848.0	43471724.0	GSM2266456 r1	0:51 1:51	A:1111247951;C:1116993636;G:1091144647;T:1114643633;N:85981	51	51	1111247951	1116993636	1091144647	1114643633	85981	SRX2011203	SRS1608491	SRA451066	GEO	University of Maryland	2	0.93493	0.93506	0.12094	0.11976	0.74953	0.75144	0.47962	0.47646	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-08-10	Larval	Larval	Heart	Cardiovascular System
41260	41260	SRR4017368	SRX2011202	SRS1608488	SRP081209	PRJNA338400	Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq	GSE85416	Transcriptome Analysis	We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues		pubmed:28455512		embryonic heart 2	GSM2266455		source name:zebrafish embryonic heart\|developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	embryonic heart 2	The flow cells were sequenced as 50×2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9	zebrafish embryonic heart		Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	GSM2266455	GSM2266455: embryonic heart 2; Danio rerio; RNA Seq	GSM2266455		1	Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2266455	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP081209			4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R1.fastq.gz 4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R2.fastq.gz	fastq fastq	3994817760.0	39164880.0	GSM2266455 r1	0:51 1:51	A:984074495;C:1022214385;G:1003461979;T:984987096;N:79805	51	51	984074495	1022214385	1003461979	984987096	79805	SRX2011202	SRS1608488	SRA451066	GEO	University of Maryland	2	0.93632	0.93575	0.12674	0.1252	0.75595	0.75649	0.53521	0.50945	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-08-10	Larval	Larval	Heart	Cardiovascular System
41261	41261	SRR4017367	SRX2011201	SRS1608490	SRP081209	PRJNA338400	Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq	GSE85416	Transcriptome Analysis	We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf adult heart of 6 mpf WIK fish and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart adult heart and adult muscle tissues		pubmed:28455512		embryonic heart 0	GSM2266454		source name:zebrafish embryonic heart\|developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	embryonic heart 0	The flow cells were sequenced as 50×2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9	zebrafish embryonic heart		Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols		developmental stage:embryo\|tissue:heart\|genotype:wild type\|age:4 days	GSM2266454	GSM2266454: embryonic heart 0; Danio rerio; RNA Seq	GSM2266454		1	Tissues were homogenized using a mortar and pestle Fisher Scientific and total RNA was extracted using TRIzol Sigma according to the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2266454	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP081209			4dpf_embryonic_heart-2.FCD29WDACXX_L6_IATCACG.bam.R1.fastq.gz 4dpf_embryonic_heart-2.FCD29WDACXX_L6_IATCACG.bam.R2.fastq.gz	fastq fastq	3803267472.0	37286936.0	GSM2266454 r1	0:51 1:51	A:931217439;C:976995973;G:962316893;T:932631659;N:105508	51	51	931217439	976995973	962316893	932631659	105508	SRX2011201	SRS1608490	SRA451066	GEO	University of Maryland	2	0.92776	0.92939	0.11824	0.11891	0.75856	0.75927	0.54225	0.5297	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-08-10	Larval	Larval	Heart	Cardiovascular System
41859	41859	SRR6384890	SRX3478480	SRS2764469	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Zfpm1 21dpf heart rep3	GSM2892215		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	Zfpm1 21dpf heart rep3	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	GSM2892215	GSM2892215: Zfpm1 21dpf heart rep3; Danio rerio; RNA Seq	GSM2892215		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892215	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Zfpm1_heart_RNAseq_rep3_1.fq.gz Zfpm1_heart_RNAseq_rep3_2.fq.gz	fastq fastq	7816015200.0	26053384.0	GSM2892215 r1	0:150 1:150	A:2069370368;C:1834259592;G:1844770941;T:2066284500;N:1329799	150	150	2069370368	1834259592	1844770941	2066284500	1329799	SRX3478480	SRS2764469	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.94934	0.95013	0.07892	0.07945	0.71727	0.72137	0.50507	0.50557	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
41860	41860	SRR6384889	SRX3478479	SRS2764468	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Zfpm1 21dpf heart rep2	GSM2892214		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	Zfpm1 21dpf heart rep2	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	GSM2892214	GSM2892214: Zfpm1 21dpf heart rep2; Danio rerio; RNA Seq	GSM2892214		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892214	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Zfpm1_heart_RNAseq_rep2_2.fq.gz Zfpm1_heart_RNAseq_rep2_1.fq.gz	fastq fastq	6730887900.0	22436293.0	GSM2892214 r1	0:150 1:150	A:1776206645;C:1586469799;G:1595359983;T:1771693512;N:1157961	150	150	1776206645	1586469799	1595359983	1771693512	1157961	SRX3478479	SRS2764468	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.94995	0.94881	0.07751	0.0776	0.7108	0.71526	0.51984	0.50583	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
41861	41861	SRR6384888	SRX3478478	SRS2764467	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Zfpm1 21dpf heart rep1	GSM2892213		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	Zfpm1 21dpf heart rep1	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:zfpm1 mutant	GSM2892213	GSM2892213: Zfpm1 21dpf heart rep1; Danio rerio; RNA Seq	GSM2892213		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892213	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Zfpm1_heart_RNAseq_rep1_1.fq.gz Zfpm1_heart_RNAseq_rep1_2.fq.gz	fastq fastq	5936614800.0	19788716.0	GSM2892213 r1	0:150 1:150	A:1616123286;C:1354032331;G:1348383945;T:1617882201;N:193037	150	150	1616123286	1354032331	1348383945	1617882201	193037	SRX3478478	SRS2764467	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.93121	0.93134	0.08641	0.08612	0.69501	0.69751	0.51182	0.50932	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
41862	41862	SRR6384887	SRX3478477	SRS2764466	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Ctrl 21dpf heart rep3	GSM2892212		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	Ctrl 21dpf heart rep3	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	GSM2892212	GSM2892212: Ctrl 21dpf heart rep3; Danio rerio; RNA Seq	GSM2892212		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892212	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Ctrl_heart_RNAseq_rep3_1.fq.gz Ctrl_heart_RNAseq_rep3_2.fq.gz	fastq fastq	6715383900.0	22384613.0	GSM2892212 r1	0:150 1:150	A:1758554869;C:1599044471;G:1608050484;T:1748581031;N:1153045	150	150	1758554869	1599044471	1608050484	1748581031	1153045	SRX3478477	SRS2764466	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.9491	0.94781	0.0799	0.07904	0.73357	0.73795	0.51407	0.50294	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
41863	41863	SRR6384886	SRX3478476	SRS2764465	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Ctrl 21dpf heart rep2	GSM2892211		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	Ctrl 21dpf heart rep2	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	GSM2892211	GSM2892211: Ctrl 21dpf heart rep2; Danio rerio; RNA Seq	GSM2892211		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892211	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Ctrl_heart_RNAseq_rep2_1.fq.gz Ctrl_heart_RNAseq_rep2_2.fq.gz	fastq fastq	7503873000.0	25012910.0	GSM2892211 r1	0:150 1:150	A:1975436432;C:1780336468;G:1790380856;T:1956431600;N:1287644	150	150	1975436432	1780336468	1790380856	1956431600	1287644	SRX3478476	SRS2764465	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.95183	0.95114	0.05969	0.05955	0.74176	0.74588	0.49341	0.49778	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
41864	41864	SRR6384885	SRX3478475	SRS2764464	SRP100425	PRJNA376117	Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development	GSE95118	Transcriptome Analysis	Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.		pubmed:30611731		Ctrl 21dpf heart rep1	GSM2892210		source name:heart\|strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	Ctrl 21dpf heart rep1	Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters q p 8 no novel juncs G o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample	heart		36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.		strain:TU\|tissue:heart\|developmental stage:21dpf\|genotype:control	GSM2892210	GSM2892210: Ctrl 21dpf heart rep1; Danio rerio; RNA Seq	GSM2892210		1	36hpf zebrafish embryos and 21dpf heart were collected respectively flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions then repaired at the tail ends polyA added and enriched by PCR amplification. Finally we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.	GEO Accession:GSM2892210	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP100425			Ctrl_heart_RNAseq_rep1_1.fq.gz Ctrl_heart_RNAseq_rep1_2.fq.gz	fastq fastq	6814864500.0	22716215.0	GSM2892210 r1	0:150 1:150	A:1866471058;C:1546350618;G:1541549692;T:1860269780;N:223352	150	150	1866471058	1546350618	1541549692	1860269780	223352	SRX3478475	SRS2764464	SRA539171	GEO	Xin Lou Lab, Medical School, Nanjing University	2	0.93945	0.94117	0.08481	0.08446	0.7359	0.73845	0.50016	0.48236	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2017-12-18	Larval	Larval	Heart	Cardiovascular System
43727	43727	SRR6039673	SRX3187841	SRS2515289	SRP117696	PRJNA407368	RNA seq timecourse analysis during zebrafish heart looping morphogenesis	PRJNA407368	Other	During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development during which many congenital heart disease malformations likely arise we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern identified transcription factor binding motifs enriched in each cluster and generated a model GRN for the major gene batteries in heart morphogenesis.					C72		time point hpf group:C\|multiplex group:4\|strain:cmlc2::gfp reporter line\|dev stage:72 hpf organism or animal									RNA Seq of Danio rerio heart tissue: Time series during heart looping 30 72 hpf	C72	C72	For each replicate approximately 1600 zebrafish embryos were collected 200 each at 30 36 42 48 54 60 66 72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at 80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP117696			9499X24_130410_SN141_0670_AD228RACXX_8.txt.gz	fastq	1232597200.0	24651944.0	9499X24 130410 SN141 0670 AD228RACXX 8.txt.gz	0:50	A:314251321;C:291544555;G:296775805;T:329828647;N:196872	50		314251321	291544555	296775805	329828647	196872	SRX3187841	SRS2515289	SRA608458	University of Utah\|Neurobiology and Anatomy	University of Utah	1	0.85915		0.19661		0.77193		0.54788		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-09-14	Larval	Larval	Heart	Cardiovascular System
43738	43738	SRR6039684	SRX3187830	SRS2515278	SRP117696	PRJNA407368	RNA seq timecourse analysis during zebrafish heart looping morphogenesis	PRJNA407368	Other	During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development during which many congenital heart disease malformations likely arise we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern identified transcription factor binding motifs enriched in each cluster and generated a model GRN for the major gene batteries in heart morphogenesis.					A72		time point hpf group:A\|multiplex group:2\|strain:cmlc2::gfp reporter line\|dev stage:72 hpf organism or animal									RNA Seq of Danio rerio heart tissue: Time series during heart looping 30 72 hpf	A72	A72	For each replicate approximately 1600 zebrafish embryos were collected 200 each at 30 36 42 48 54 60 66 72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at 80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP117696			9499X8_130405_SN141_0668_AD2154ACXX_8.txt.gz	fastq	1245726350.0	24914527.0	9499X8 130405 SN141 0668 AD2154ACXX 8.txt.gz	0:50	A:289841562;C:326831788;G:324971093;T:303973349;N:108558	50		289841562	326831788	324971093	303973349	108558	SRX3187830	SRS2515278	SRA608458	University of Utah\|Neurobiology and Anatomy	University of Utah	1	0.33366		0.08879		0.88994		0.71252		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-09-14	Larval	Larval	Heart	Cardiovascular System
43742	43742	SRR6039688	SRX3187826	SRS2515275	SRP117696	PRJNA407368	RNA seq timecourse analysis during zebrafish heart looping morphogenesis	PRJNA407368	Other	During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development during which many congenital heart disease malformations likely arise we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern identified transcription factor binding motifs enriched in each cluster and generated a model GRN for the major gene batteries in heart morphogenesis.					B72		time point hpf group:B\|multiplex group:3\|strain:cmlc2::gfp reporter line\|dev stage:72 hpf organism or animal									RNA Seq of Danio rerio heart tissue: Time series during heart looping 30 72 hpf	B72	B72	For each replicate approximately 1600 zebrafish embryos were collected 200 each at 30 36 42 48 54 60 66 72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at 80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP117696			9499X16_130410_SN141_0670_AD228RACXX_7.txt.gz	fastq	1454189100.0	29083782.0	9499X16 130410 SN141 0670 AD228RACXX 7.txt.gz	0:50	A:351566404;C:363298465;G:371864963;T:367228366;N:230902	50		351566404	363298465	371864963	367228366	230902	SRX3187826	SRS2515275	SRA608458	University of Utah\|Neurobiology and Anatomy	University of Utah	1	0.86742		0.18808		0.80018		0.7503		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2017-09-14	Larval	Larval	Heart	Cardiovascular System
46217	46217	SRR6506181	SRX3594765	SRS2867192	SRP131362	PRJNA431371	Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes	GSE109553	Transcriptome Analysis	Heart tissue mRNA profiles of 50 wild type WT and 50 homozygous smyd4 mutant zebrafish embryos at 72 hpf created by CRISPR/Cas9 were generated by deep sequencing. Overall design: Heart mRNA profiles of 72 hpf wild type WT and smdy4 mutant zebrafish were generated by deep sequencing using illumina				smyd4	GSM2946171		source name:heart\|tissue:heart\|strain:Tu\|age:72 hpf\|genotype:homozygous smyd4 L544Efs*1	smyd4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Bowtie v2.0.6 and paired end clean reads were aligned to the reference genome using TopHat v2.0.9. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene considering the effect of sequencing depth and gene length for the reads count at the same time Mortazavi et al. 2008 Genome build: ftp://ftp.ensembl.org/pub/release 89/fasta/danio rerio/dna/ Supplementary files format and content: text file with RPKM	heart		zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:heart\|strain:Tu\|age:72 hpf\|genotype:homozygous smyd4 L544Efs*1	GSM2946171	GSM2946171: smyd4; Danio rerio; RNA Seq	GSM2946171		1	zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2946171	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP131362			smyd4_zf_1.fq.gz smyd4_zf_2.fq.gz	fastq fastq	7954641600.0	26515472.0	GSM2946171 r1	0:150 1:150	A:2150119275;C:1788273579;G:1800637070;T:2214193156;N:1418520	150	150	2150119275	1788273579	1800637070	2214193156	1418520	SRX3594765	SRS2867192	SRA651951	GEO	Fudan university	2	0.95241	0.94978	0.06519	0.06325	0.70838	0.71587	0.42753	0.42209	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2018-01-24	Larval	Larval	Heart	Cardiovascular System
46218	46218	SRR6506180	SRX3594764	SRS2867189	SRP131362	PRJNA431371	Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes	GSE109553	Transcriptome Analysis	Heart tissue mRNA profiles of 50 wild type WT and 50 homozygous smyd4 mutant zebrafish embryos at 72 hpf created by CRISPR/Cas9 were generated by deep sequencing. Overall design: Heart mRNA profiles of 72 hpf wild type WT and smdy4 mutant zebrafish were generated by deep sequencing using illumina				wt	GSM2946170		source name:heart\|tissue:heart\|strain:Tu\|age:72 hpf\|genotype:wt	wt	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Bowtie v2.0.6 and paired end clean reads were aligned to the reference genome using TopHat v2.0.9. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene considering the effect of sequencing depth and gene length for the reads count at the same time Mortazavi et al. 2008 Genome build: ftp://ftp.ensembl.org/pub/release 89/fasta/danio rerio/dna/ Supplementary files format and content: text file with RPKM	heart		zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:heart\|strain:Tu\|age:72 hpf\|genotype:wt	GSM2946170	GSM2946170: wt; Danio rerio; RNA Seq	GSM2946170		1	zebrafish heart were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2946170	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten	SRP131362			ctr_zf_1.fq.gz ctr_zf_2.fq.gz	fastq fastq	9601941900.0	32006473.0	GSM2946170 r1	0:150 1:150	A:2440007788;C:2202792595;G:2248095757;T:2709447485;N:1598275	150	150	2440007788	2202792595	2248095757	2709447485	1598275	SRX3594764	SRS2867189	SRA651951	GEO	Fudan university	2	0.93538	0.92842	0.05404	0.04218	0.7387	0.75866	0.43777	0.42189	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2018-01-24	Larval	Larval	Heart	Cardiovascular System
48190	48190	SRR7119875	SRX4041518	SRS3258997	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 44	GSM3131266		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 44	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131266	GSM3131266: Danio rerio RNAseq singleHeart 3dpf mut 44; Danio rerio; RNA Seq	GSM3131266		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131266	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_44_NDCII_sample_0044.fastq.gz	fastq	182748450.0	2436646.0	GSM3131266 r1	0:75	A:58073626;C:30410206;G:39711272;T:54442336;N:111010	75		58073626	30410206	39711272	54442336	111010	SRX4041518	SRS3258997	SRA699717	GEO	Molecular Biology, Radboud University	1	0.60972		0.21593		0.85427		0.51332		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48191	48191	SRR7119874	SRX4041517	SRS3258996	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 43	GSM3131265		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 43	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131265	GSM3131265: Danio rerio RNAseq singleHeart 3dpf mut 43; Danio rerio; RNA Seq	GSM3131265		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131265	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_43_NDCII_sample_0043.fastq.gz	fastq	91153575.0	1215381.0	GSM3131265 r1	0:75	A:29202562;C:14935465;G:19738048;T:27228137;N:49363	75		29202562	14935465	19738048	27228137	49363	SRX4041517	SRS3258996	SRA699717	GEO	Molecular Biology, Radboud University	1	0.61061		0.18268		0.87257		0.51994		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48192	48192	SRR7119873	SRX4041516	SRS3258995	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 42	GSM3131264		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 42	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131264	GSM3131264: Danio rerio RNAseq singleHeart 3dpf mut 42; Danio rerio; RNA Seq	GSM3131264		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131264	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_42_NDCII_sample_0042.fastq.gz	fastq	213129525.0	2841727.0	GSM3131264 r1	0:75	A:66201701;C:36179557;G:46211697;T:64412897;N:123673	75		66201701	36179557	46211697	64412897	123673	SRX4041516	SRS3258995	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62509		0.23068		0.85397		0.4951		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48193	48193	SRR7119872	SRX4041515	SRS3258994	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 41	GSM3131263		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 41	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131263	GSM3131263: Danio rerio RNAseq singleHeart 3dpf mut 41; Danio rerio; RNA Seq	GSM3131263		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131263	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_41_NDCII_sample_0041.fastq.gz	fastq	166984800.0	2226464.0	GSM3131263 r1	0:75	A:52059221;C:28218639;G:36132669;T:50478431;N:95840	75		52059221	28218639	36132669	50478431	95840	SRX4041515	SRS3258994	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64245		0.22817		0.86535		0.4946		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48194	48194	SRR7119871	SRX4041514	SRS3258992	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 40	GSM3131262		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 40	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131262	GSM3131262: Danio rerio RNAseq singleHeart 3dpf mut 40; Danio rerio; RNA Seq	GSM3131262		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131262	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_40_NDCII_sample_0040.fastq.gz	fastq	76091325.0	1014551.0	GSM3131262 r1	0:75	A:23961767;C:13365431;G:16139381;T:22578835;N:45911	75		23961767	13365431	16139381	22578835	45911	SRX4041514	SRS3258992	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68263		0.15501		0.86642		0.45686		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48195	48195	SRR7119870	SRX4041513	SRS3258993	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 39	GSM3131261		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 39	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131261	GSM3131261: Danio rerio RNAseq singleHeart 3dpf mut 39; Danio rerio; RNA Seq	GSM3131261		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131261	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_39_NDCII_sample_0039.fastq.gz	fastq	83697825.0	1115971.0	GSM3131261 r1	0:75	A:25833162;C:14319026;G:18237724;T:25260425;N:47488	75		25833162	14319026	18237724	25260425	47488	SRX4041513	SRS3258993	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68511		0.1681		0.87359		0.50056		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48196	48196	SRR7119869	SRX4041512	SRS3258991	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 38	GSM3131260		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 38	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131260	GSM3131260: Danio rerio RNAseq singleHeart 3dpf mut 38; Danio rerio; RNA Seq	GSM3131260		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131260	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_38_NDCII_sample_0038.fastq.gz	fastq	89200050.0	1189334.0	GSM3131260 r1	0:75	A:27880894;C:15422868;G:19386687;T:26456153;N:53448	75		27880894	15422868	19386687	26456153	53448	SRX4041512	SRS3258991	SRA699717	GEO	Molecular Biology, Radboud University	1	0.63181		0.17615		0.86736		0.5058		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48197	48197	SRR7119868	SRX4041511	SRS3258989	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 37	GSM3131259		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 37	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131259	GSM3131259: Danio rerio RNAseq singleHeart 3dpf mut 37; Danio rerio; RNA Seq	GSM3131259		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131259	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_37_NDCII_sample_0037.fastq.gz	fastq	144136050.0	1921814.0	GSM3131259 r1	0:75	A:45236020;C:23884461;G:31356238;T:43570898;N:88433	75		45236020	23884461	31356238	43570898	88433	SRX4041511	SRS3258989	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64128		0.19693		0.86734		0.54791		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48198	48198	SRR7119867	SRX4041510	SRS3258990	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf mut 36	GSM3131258		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	Danio rerio RNAseq singleHeart 3dpf mut 36	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2 /	GSM3131258	GSM3131258: Danio rerio RNAseq singleHeart 3dpf mut 36; Danio rerio; RNA Seq	GSM3131258		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131258	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_36_NDCII_sample_0036.fastq.gz	fastq	98485275.0	1313137.0	GSM3131258 r1	0:75	A:31078665;C:16821229;G:21507034;T:29019964;N:58383	75		31078665	16821229	21507034	29019964	58383	SRX4041510	SRS3258990	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62906		0.24825		0.86592		0.56159		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48208	48208	SRR7119857	SRX4041500	SRS3258979	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 24	GSM3131248		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 24	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131248	GSM3131248: Danio rerio RNAseq singleHeart 3dpf wt 24; Danio rerio; RNA Seq	GSM3131248		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131248	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_24_NDCII_sample_0024.fastq.gz	fastq	56268825.0	750251.0	GSM3131248 r1	0:75	A:17328594;C:9907009;G:12451765;T:16549368;N:32089	75		17328594	9907009	12451765	16549368	32089	SRX4041500	SRS3258979	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68698		0.13156		0.87647		0.54659		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48209	48209	SRR7119856	SRX4041499	SRS3258978	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 23	GSM3131247		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 23	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131247	GSM3131247: Danio rerio RNAseq singleHeart 3dpf wt 23; Danio rerio; RNA Seq	GSM3131247		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131247	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_23_NDCII_sample_0023.fastq.gz	fastq	113729700.0	1516396.0	GSM3131247 r1	0:75	A:34708329;C:19742375;G:24997702;T:34216965;N:64329	75		34708329	19742375	24997702	34216965	64329	SRX4041499	SRS3258978	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68965		0.1358		0.86168		0.50041		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48210	48210	SRR7119855	SRX4041498	SRS3258976	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 22	GSM3131246		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 22	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131246	GSM3131246: Danio rerio RNAseq singleHeart 3dpf wt 22; Danio rerio; RNA Seq	GSM3131246		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131246	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_22_NDCII_sample_0022.fastq.gz	fastq	129788625.0	1730515.0	GSM3131246 r1	0:75	A:39826852;C:22345144;G:28340986;T:39198043;N:77600	75		39826852	22345144	28340986	39198043	77600	SRX4041498	SRS3258976	SRA699717	GEO	Molecular Biology, Radboud University	1	0.68637		0.19709		0.85662		0.52926		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48211	48211	SRR7119854	SRX4041497	SRS3258975	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 21	GSM3131245		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 21	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131245	GSM3131245: Danio rerio RNAseq singleHeart 3dpf wt 21; Danio rerio; RNA Seq	GSM3131245		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131245	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_21_NDCII_sample_0021.fastq.gz	fastq	74830575.0	997741.0	GSM3131245 r1	0:75	A:23292108;C:12771005;G:16485526;T:22236863;N:45073	75		23292108	12771005	16485526	22236863	45073	SRX4041497	SRS3258975	SRA699717	GEO	Molecular Biology, Radboud University	1	0.62409		0.23647		0.88398		0.52649		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48212	48212	SRR7119853	SRX4041496	SRS3258974	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 20	GSM3131244		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 20	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131244	GSM3131244: Danio rerio RNAseq singleHeart 3dpf wt 20; Danio rerio; RNA Seq	GSM3131244		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131244	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_20_NDCII_sample_0020.fastq.gz	fastq	83202075.0	1109361.0	GSM3131244 r1	0:75	A:26090654;C:14537361;G:18178302;T:24348215;N:47543	75		26090654	14537361	18178302	24348215	47543	SRX4041496	SRS3258974	SRA699717	GEO	Molecular Biology, Radboud University	1	0.59091		0.18382		0.87274		0.50189		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48213	48213	SRR7119852	SRX4041495	SRS3258973	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 19	GSM3131243		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 19	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131243	GSM3131243: Danio rerio RNAseq singleHeart 3dpf wt 19; Danio rerio; RNA Seq	GSM3131243		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131243	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_19_NDCII_sample_0019.fastq.gz	fastq	61352025.0	818027.0	GSM3131243 r1	0:75	A:19173237;C:10426603;G:13570586;T:18144746;N:36853	75		19173237	10426603	13570586	18144746	36853	SRX4041495	SRS3258973	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64995		0.19171		0.87213		0.54952		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48214	48214	SRR7119851	SRX4041494	SRS3258972	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 18	GSM3131242		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 18	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131242	GSM3131242: Danio rerio RNAseq singleHeart 3dpf wt 18; Danio rerio; RNA Seq	GSM3131242		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131242	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_18_NDCII_sample_0018.fastq.gz	fastq	55114425.0	734859.0	GSM3131242 r1	0:75	A:17302961;C:9444084;G:12256958;T:16079162;N:31260	75		17302961	9444084	12256958	16079162	31260	SRX4041494	SRS3258972	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64027		0.2383		0.87903		0.53857		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48215	48215	SRR7119850	SRX4041493	SRS3258971	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 17	GSM3131241		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 17	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131241	GSM3131241: Danio rerio RNAseq singleHeart 3dpf wt 17; Danio rerio; RNA Seq	GSM3131241		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131241	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_17_NDCII_sample_0017.fastq.gz	fastq	54385575.0	725141.0	GSM3131241 r1	0:75	A:17178884;C:9154385;G:11956346;T:16062768;N:33192	75		17178884	9154385	11956346	16062768	33192	SRX4041493	SRS3258971	SRA699717	GEO	Molecular Biology, Radboud University	1	0.6122		0.27421		0.88552		0.5705		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48216	48216	SRR7119849	SRX4041492	SRS3258970	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 16	GSM3131240		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 16	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131240	GSM3131240: Danio rerio RNAseq singleHeart 3dpf wt 16; Danio rerio; RNA Seq	GSM3131240		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131240	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_16_NDCII_sample_0016.fastq.gz	fastq	68361225.0	911483.0	GSM3131240 r1	0:75	A:20763268;C:11958924;G:16351810;T:19246084;N:41139	75		20763268	11958924	16351810	19246084	41139	SRX4041492	SRS3258970	SRA699717	GEO	Molecular Biology, Radboud University	1	0.64264		0.12251		0.88477		0.57059		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
48217	48217	SRR7119848	SRX4041491	SRS3258969	SRP144601	PRJNA459724	The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis	GSE114038	Other	Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1 2 3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos wild types and rnf2 mutants 8 and 7 replicates respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1 2 dpf and 3 dpf Danio rerio dissected hearts wild types 9 13 and 10 replicates respectively and rnf2 mutants 8 9 and 9 replicates respectively		pubmed:30867528		Danio rerio RNAseq singleHeart 3dpf wt 15	GSM3131239		tissue:heart\|strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	Danio rerio RNAseq singleHeart 3dpf wt 15	RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format	heart		RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain:TU/TLF mixed background\|cell type:heart\|age:3dpf\|genotype:myl7:GFP rnf2+/+	GSM3131239	GSM3131239: Danio rerio RNAseq singleHeart 3dpf wt 15; Danio rerio; RNA Seq	GSM3131239		1	RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation	GEO Accession:GSM3131239	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP144601			NDCII_1_15_NDCII_sample_0015.fastq.gz	fastq	43246350.0	576618.0	GSM3131239 r1	0:75	A:13423239;C:7409151;G:9733956;T:12657584;N:22420	75		13423239	7409151	9733956	12657584	22420	SRX4041491	SRS3258969	SRA699717	GEO	Molecular Biology, Radboud University	1	0.66495		0.14227		0.88828		0.56869		75		B		usable mapping rate	illumina	nextseq	unknown	rrna_depletion	ribozero	sc	single_cell_plate	celseq	Netherlands	2018-05-04	Larval	Larval	Heart	Cardiovascular System
49040	49040	SRR7633494	SRX4497225	SRS3618225	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G2 endo 03	GSM3317066		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317066	GSM3317066: G2 endo 03; Danio rerio; RNA Seq	GSM3317066		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317066	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S18_trimmed.fastq.gz	fastq	950344310.0	18847513.0	GSM3317066 r1	0:50.42 1:0	A:270135652;C:209210468;G:202674675;T:268256430;N:67085	50	0	270135652	209210468	202674675	268256430	67085	SRX4497225	SRS3618225	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89759		0.1428		0.69132		0.4729		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49041	49041	SRR7633493	SRX4497224	SRS3618224	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G2 endo 02	GSM3317065		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317065	GSM3317065: G2 endo 02; Danio rerio; RNA Seq	GSM3317065		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317065	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S17_trimmed.fastq.gz	fastq	1635110054.0	32380584.0	GSM3317065 r1	0:50.50 1:0	A:462134552;C:361057634;G:349465446;T:462337205;N:115217	50	0	462134552	361057634	349465446	462337205	115217	SRX4497224	SRS3618224	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.80201		0.12711		0.70471		0.44427		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49042	49042	SRR7633492	SRX4497223	SRS3618223	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G2 endo 01	GSM3317064		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G2 mRNA	G2 endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G2 mRNA	GSM3317064	GSM3317064: G2 endo 01; Danio rerio; RNA Seq	GSM3317064		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317064	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S16_trimmed.fastq.gz	fastq	1302352614.0	25794210.0	GSM3317064 r1	0:50.49 1:0	A:370194702;C:286011167;G:276758200;T:369297736;N:90809	50	0	370194702	286011167	276758200	369297736	90809	SRX4497223	SRS3618223	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89468		0.15745		0.69447		0.47938		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49043	49043	SRR7633491	SRX4497222	SRS3618222	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G0 endo 03	GSM3317063		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317063	GSM3317063: G0 endo 03; Danio rerio; RNA Seq	GSM3317063		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317063	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S15_trimmed.fastq.gz	fastq	1248556473.0	24725241.0	GSM3317063 r1	0:50.50 1:0	A:350256976;C:280431139;G:270771772;T:347009294;N:87292	50	0	350256976	280431139	270771772	347009294	87292	SRX4497222	SRS3618222	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.90514		0.13266		0.69236		0.47977		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49044	49044	SRR7633490	SRX4497221	SRS3618221	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G0 endo 02	GSM3317062		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317062	GSM3317062: G0 endo 02; Danio rerio; RNA Seq	GSM3317062		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317062	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S14_trimmed.fastq.gz	fastq	372093672.0	7456111.0	GSM3317062 r1	0:49.90 1:0	A:113486766;C:74400549;G:71245468;T:112935661;N:25228	49	0	113486766	74400549	71245468	112935661	25228	SRX4497221	SRS3618221	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.89644		0.12968		0.70658		0.47231		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49045	49045	SRR7633489	SRX4497220	SRS3618220	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		G0 endo 01	GSM3317061		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:human APOL1 G0 mRNA	G0 endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:human APOL1 G0 mRNA	GSM3317061	GSM3317061: G0 endo 01; Danio rerio; RNA Seq	GSM3317061		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317061	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S13_trimmed.fastq.gz	fastq	1450133780.0	28705598.0	GSM3317061 r1	0:50.52 1:0	A:407543677;C:323333189;G:313321100;T:405835253;N:100561	50	0	407543677	323333189	313321100	405835253	100561	SRX4497220	SRS3618220	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8994		0.13347		0.6942		0.47759		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49046	49046	SRR7633488	SRX4497219	SRS3618219	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		control endo 03	GSM3317060		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 03	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317060	GSM3317060: control endo 03; Danio rerio; RNA Seq	GSM3317060		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317060	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S12_trimmed.fastq.gz	fastq	1720199608.0	34019943.0	GSM3317060 r1	0:50.56 1:0	A:474252335;C:393152371;G:382256277;T:470417173;N:121452	50	0	474252335	393152371	382256277	470417173	121452	SRX4497219	SRS3618219	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.90252		0.11709		0.69668		0.47424		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49047	49047	SRR7633487	SRX4497218	SRS3618218	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		control endo 02	GSM3317059		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 02	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317059	GSM3317059: control endo 02; Danio rerio; RNA Seq	GSM3317059		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317059	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S11_trimmed.fastq.gz	fastq	322327295.0	6605687.0	GSM3317059 r1	0:48.80 1:0	A:109722776;C:53179948;G:51091267;T:108312123;N:21181	48	0	109722776	53179948	51091267	108312123	21181	SRX4497218	SRS3618218	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.8922		0.1261		0.72811		0.46128		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49048	49048	SRR7633486	SRX4497217	SRS3618217	SRP155992	PRJNA483985	Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA	GSE118000	Transcriptome Analysis	We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2		pubmed:31158233		control endo 01	GSM3317058		tissue:zebrafish endothelium\|line:fli:EGFP\|treatment:control	control endo 01	Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2	zebrafish endothelium	Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf	line:fli:EGFP\|treatment:control	GSM3317058	GSM3317058: control endo 01; Danio rerio; RNA Seq	GSM3317058		1	RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech	GEO Accession:GSM3317058	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP155992			BA_S10_trimmed.fastq.gz	fastq	1484074935.0	29385409.0	GSM3317058 r1	0:50.50 1:0	A:411414710;C:336260838;G:326730208;T:409563857;N:105322	50	0	411414710	336260838	326730208	409563857	105322	SRX4497217	SRS3618217	SRA749599	GEO	Duke Molecular Physiology Institute, Duke University Medical Center	1	0.88777		0.11462		0.70102		0.47353		49		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_plate	smartseq	United States	2018-08-01	Larval	Larval	Endothelium	Cardiovascular System
49850	49850	SRR8883829	SRX5669659	SRS4612528	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		148 2 E12 KOcxcl12a 6 reseq	GSM3719057		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	148 2 E12 KOcxcl12a 6 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719057	GSM3719057: 148 2 E12 KOcxcl12a 6 reseq; Danio rerio; RNA Seq	GSM3719057		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719057	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			148-2-E12-KOcxcl12a-6_reseq_all_lanes_R1.fastq.gz	fastq	763065205.0	10372479.0	GSM3719057 r1	0:73.57 1:0	A:179985921;C:199425581;G:205920814;T:177110327;N:622562	73	0	179985921	199425581	205920814	177110327	622562	SRX5669659	SRS4612528	SRA798477	GEO	University of Oxford	1	0.93161		0.2297		0.75684		0.64613		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49851	49851	SRR8883828	SRX5669658	SRS4612527	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		147 2 E11 KOcxcl12a 5 reseq	GSM3719056		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	147 2 E11 KOcxcl12a 5 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719056	GSM3719056: 147 2 E11 KOcxcl12a 5 reseq; Danio rerio; RNA Seq	GSM3719056		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719056	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			147-2-E11-KOcxcl12a-5_reseq_all_lanes_R1.fastq.gz	fastq	777154556.0	10544824.0	GSM3719056 r1	0:73.70 1:0	A:182318789;C:204282719;G:210781481;T:179272833;N:498734	73	0	182318789	204282719	210781481	179272833	498734	SRX5669658	SRS4612527	SRA798477	GEO	University of Oxford	1	0.94256		0.25229		0.76781		0.67336		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49852	49852	SRR8883827	SRX5669657	SRS4612526	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		146 2 E10 KOcxcl12a 4 reseq	GSM3719055		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	146 2 E10 KOcxcl12a 4 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719055	GSM3719055: 146 2 E10 KOcxcl12a 4 reseq; Danio rerio; RNA Seq	GSM3719055		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719055	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			146-2-E10-KOcxcl12a-4_reseq_all_lanes_R1.fastq.gz	fastq	893756036.0	12231836.0	GSM3719055 r1	0:73.07 1:0	A:208987215;C:235365706;G:243090724;T:205234077;N:1078314	73	0	208987215	235365706	243090724	205234077	1078314	SRX5669657	SRS4612526	SRA798477	GEO	University of Oxford	1	0.93675		0.21776		0.76597		0.63391		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49853	49853	SRR8883826	SRX5669656	SRS4612525	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		145 2 E09 KOcxcl12a 3 reseq	GSM3719054		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	145 2 E09 KOcxcl12a 3 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719054	GSM3719054: 145 2 E09 KOcxcl12a 3 reseq; Danio rerio; RNA Seq	GSM3719054		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719054	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			145-2-E09-KOcxcl12a-3_reseq_all_lanes_R1.fastq.gz	fastq	850857048.0	11668488.0	GSM3719054 r1	0:72.92 1:0	A:205769666;C:217594988;G:223805195;T:202463052;N:1224147	72	0	205769666	217594988	223805195	202463052	1224147	SRX5669656	SRS4612525	SRA798477	GEO	University of Oxford	1	0.92738		0.2566		0.75152		0.65144		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49854	49854	SRR8883825	SRX5669655	SRS4612524	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		144 2 E08 KOcxcl12a 2 reseq	GSM3719053		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	144 2 E08 KOcxcl12a 2 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719053	GSM3719053: 144 2 E08 KOcxcl12a 2 reseq; Danio rerio; RNA Seq	GSM3719053		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719053	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			144-2-E08-KOcxcl12a-2_reseq_all_lanes_R1.fastq.gz	fastq	898577334.0	12271421.0	GSM3719053 r1	0:73.23 1:0	A:209765901;C:237376777;G:244548553;T:205953258;N:932845	73	0	209765901	237376777	244548553	205953258	932845	SRX5669655	SRS4612524	SRA798477	GEO	University of Oxford	1	0.94312		0.22115		0.75751		0.63782		72		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49855	49855	SRR8883824	SRX5669654	SRS4612523	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		143 2 E07 KOcxcl12a 1 reseq	GSM3719052		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	143 2 E07 KOcxcl12a 1 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719052	GSM3719052: 143 2 E07 KOcxcl12a 1 reseq; Danio rerio; RNA Seq	GSM3719052		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719052	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			143-2-E07-KOcxcl12a-1_reseq_all_lanes_R1.fastq.gz	fastq	642191206.0	8724687.0	GSM3719052 r1	0:73.61 1:0	A:148702964;C:170638392;G:176459501;T:145895525;N:494824	73	0	148702964	170638392	176459501	145895525	494824	SRX5669654	SRS4612523	SRA798477	GEO	University of Oxford	1	0.93805		0.20319		0.76203		0.65533		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49856	49856	SRR8883823	SRX5669653	SRS4612522	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		142 2 E06 KOcxcl12a ctr 3 reseq	GSM3719051		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	142 2 E06 KOcxcl12a ctr 3 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719051	GSM3719051: 142 2 E06 KOcxcl12a ctr 3 reseq; Danio rerio; RNA Seq	GSM3719051		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719051	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			142-2-E06-KOcxcl12a-ctr-3_reseq_all_lanes_R1.fastq.gz	fastq	913646709.0	12532356.0	GSM3719051 r1	0:72.90 1:0	A:210664396;C:243042644;G:251444631;T:207071337;N:1423701	72	0	210664396	243042644	251444631	207071337	1423701	SRX5669653	SRS4612522	SRA798477	GEO	University of Oxford	1	0.93582		0.21132		0.7669		0.65882		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System
49857	49857	SRR8883822	SRX5669652	SRS4612521	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		141 2 E05 KOcxcl12a ctr 2 reseq	GSM3719050		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	141 2 E05 KOcxcl12a ctr 2 reseq	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3719050	GSM3719050: 141 2 E05 KOcxcl12a ctr 2 reseq; Danio rerio; RNA Seq	GSM3719050		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3719050	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP166782			141-2-E05-KOcxcl12a-ctr-2_reseq_all_lanes_R1.fastq.gz	fastq	698256933.0	9557079.0	GSM3719050 r1	0:73.06 1:0	A:165636445;C:181576831;G:187431558;T:162693862;N:918237	73	0	165636445	181576831	187431558	162693862	918237	SRX5669652	SRS4612521	SRA798477	GEO	University of Oxford	1	0.92623		0.20301		0.75562		0.58643		74		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System

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