metadata: run_metadata: 34 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RANDOM" and tissue

34 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RANDOM" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
8088	8088	ERR034127	ERX012653	ERS032268	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 50% epiboly stage	zebrafish embryo 50 epiboly	SAMEA791629	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791629\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 50epiboly	JKE Drerio rna seq	Transcriptome profiling of 50% epiboly stages of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz	SOLiD_native SOLiD_native	3929903550.0	78598071.0	KI BN JKE DRERIO RNASEQ 2011 50epiboly	0:50		50							ERX012653	ERS032268	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.60757		0.09893		0.94899		0.77821		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
8089	8089	ERR034126	ERX012652	ERS032267	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 512 cell stage	zebrafish embryo 512 cell	SAMEA791632	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791632\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 512cell	JKE Drerio rna seq	Transcriptome profiling of 512 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz	SOLiD_native SOLiD_native	3918756250.0	78375125.0	KI BN JKE DRERIO RNASEQ 2011 512cell	0:50		50							ERX012652	ERS032267	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.63824		0.09111		0.91969		0.73496		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Blastula	Embryo	Embryo Imprecise	All anatomical structures
8090	8090	ERR034125	ERX012651	ERS032266	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 16 cell stage	zebrafish embryo 16 cell	SAMEA791631	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791631\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 16cell	JKE Drerio rna seq	Transcriptome profiling of 16 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz	SOLiD_native SOLiD_native	4256756500.0	85135130.0	KI BN JKE DRERIO RNASEQ 2011 16cell	0:50		50							ERX012651	ERS032266	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.57946		0.08115		0.91896		0.72164		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
8091	8091	ERR034124	ERX012650	ERS032265	ERP000635	PRJEB2512	The Zebrafish transcriptome during early development	KI-BN-JKE-DRERIO-RNASEQ-2011	Transcriptome Analysis	Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.		RNA extracted from zebrafish embryo at 1 cell stage	zebrafish embryo 1 cell	SAMEA791630	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	ENA first public:2011 06 09\|ENA last update:2018 03 08\|External Id:SAMEA791630\|INSDC center alias:KI BN\|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden\|INSDC first public:2011 06 09T11:04:10Z\|INSDC last update:2018 03 08T15:26:39Z\|INSDC status:public\|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell\|common name:zebrafish\|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell\|sex:mixed\|strain:Tuebingen	Transcriptome profiling of early zebrafish development	KI BN JKE DRERIO RNASEQ 2011 1cell	JKE Drerio rna seq	Transcriptome profiling of 1 cell stage of zebrafish embryos.	Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.		RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP000635	AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development	ENA FIRST PUBLIC:2011 06 09\|ENA LAST UPDATE:2018 11 16	KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz	SOLiD_native SOLiD_native	3676380950.0	73527619.0	KI BN JKE DRERIO RNASEQ 2011 1cell	0:50		50							ERX012650	ERS032265	ERA029959	KI-BN\|Department of Biosciences and Nutrition	Department of Biosciences and Nutrition, Karolinska Institutet, Sweden	1	0.64855		0.08432		0.9052		0.74223		50		B		usable mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	Sweden	2011-06-09	Zygote	Embryo	Embryo Imprecise	All anatomical structures
10060	10060	ERR4795364	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz	fastq	5410723202.0	71707309.0	E MTAB 9727:Sample 4	0:75.46 1:0	A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666	75	0	1330416803	531269504	734031980	2814959249	45666	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.33614		0.21532		0.99019		0.41002		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10061	10061	ERR4795365	ERX4665135	ERS5281176	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 4	E MTAB 9727:Sample 4		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 4 s	Sample 4 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 4	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz	fastq	5414184547.0	71707309.0	E MTAB 9727:Sample 4 1	0:0 1:75.50	A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967	0	75	1582938104	1052565419	1177180395	1600161662	1338967	ERX4665135	ERS5281176	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.84976		0.28521		0.85038		0.5124		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10062	10062	ERR4795362	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz	fastq	4823193891.0	63965519.0	E MTAB 9727:Sample 3	0:75.40 1:0	A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086	75	0	1323978162	446831209	581746343	2470114091	524086	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.36549		0.19722		0.95552		0.4702		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10063	10063	ERR4795363	ERX4665134	ERS5281175	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 3	E MTAB 9727:Sample 3		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 3 s	Sample 3 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 3	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz	fastq	4828889391.0	63965519.0	E MTAB 9727:Sample 3 1	0:0 1:75.49	A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756	0	75	1434099697	964508763	893584575	1534727600	1968756	ERX4665134	ERS5281175	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.85811		0.26231		0.82731		0.48618		76		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10064	10064	ERR4795360	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz	fastq	5598371393.0	74235388.0	E MTAB 9727:Sample 2	0:75.41 1:0	A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655	75	0	1526486973	558020193	717587491	2795646081	630655	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.28059		0.19252		0.96404		0.4874		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10065	10065	ERR4795361	ERX4665133	ERS5281174	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 2	E MTAB 9727:Sample 2		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 2 s	Sample 2 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz	fastq	5600151371.0	74235388.0	E MTAB 9727:Sample 2 1	0:0 1:75.44	A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060	0	75	1850568176	1035622971	1071138281	1640475883	2346060	ERX4665133	ERS5281174	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.7679		0.30371		0.82651		0.43401		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10066	10066	ERR4795358	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz	fastq	4996502316.0	66258508.0	E MTAB 9727:Sample 1	0:75.41 1:0	A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936	75	0	1330744174	451622042	591151500	2622422664	561936	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.29754		0.17671		0.9669		0.45463		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
10067	10067	ERR4795359	ERX4665132	ERS5281173	ERP124847	PRJEB41113	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E-MTAB-9727	Transcriptome Analysis	The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans…	Sample 1	E MTAB 9727:Sample 1		isolate:not applicable\|organism:Danio rerio\|sex:mixed\|age:10\|developmental stage:tailbud stage\|organism part:lateral plate mesoderm plate\|genotype:drl:mCherry\|ENA FIRST PUBLIC:2021 04 01\|ENA LAST UPDATE:2021 09 01	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	E MTAB 9727:Sample 1 s	Sample 1 s	Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an…	Experimental Factor: replicate:lateral plate mesoderm plate 1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	SINGLE	ILLUMINA	NextSeq 500		ERP124847	NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz	fastq	4999908389.0	66258508.0	E MTAB 9727:Sample 1 1	0:0 1:75.46	A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512	0	75	1591945117	933968124	986108614	1485824022	2062512	ERX4665132	ERS5281173	ERA3048543	University of Zurich\|European Nucleotide Archive	University of Zurich\|European Nucleotide Archive	1	0.81333		0.2466		0.83027		0.51572		75		B		usable mapping rate	illumina	nextseq	unknown	random_priming	trueseq	sc	single_cell_plate	celseq	Switzerland	2021-04-01	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
32370	32370	SRR29180530	SRX24700714	SRS21428245	SRP509851	PRJNA1116337	Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish	PRJNA1116337	Other	Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.				DES		isolate:exposure to DES\|age:48 hpf\|dev stage:embryos\|collection date:2018 06\|geo loc name:Portugal\|sex:pooled male and female\|tissue:embryos\|treatment:exposure to DES\|BioSampleModel:Model organism or animal	RNA seq of DES treated	DES	DES	Sequencing the transcriptomes of zebrafish embryos of DES treated			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP509851			DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz	fastq fastq	9169560000.0	30565200.0	DES TAAGGC L001 R1 001.fastq.gz	0:150 1:150	A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630	150	150	2545096687	2037322055	2024787099	2562124529	229630	SRX24700714	SRS21428245	SRA1878028	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University												B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2024-05-25	Hatching	Embryo	Embryo Imprecise	All anatomical structures
41782	41782	SRR5162099	SRX2480053	SRS1910957	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					PLC5shCtrl1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:PLC5shCtrl1\|BioSampleModel:Model organism or animal	PLC5shCtrl1	PLC5shCtrl1	PLC5shCtrl1	Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1201388650.0	24027773.0	CL100006841 L02 24 1.fq.gz	0:50	A:297299471;C:292335863;G:332701724;T:278571616;N:479976	50		297299471	292335863	332701724	278571616	479976	SRX2480053	SRS1910957	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00295		0.00039		0.99754		0.63223		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
41783	41783	SRR5162098	SRX2480052	SRS1910956	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					Hep3BshS6K1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:Hep3BshS6K1\|BioSampleModel:Model organism or animal	Hep3BshS6K1	Hep3BshS6K1	Hep3BshS6K1	Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1205347750.0	24106955.0	CL100006841 L02 21 1.fq.gz	0:50	A:312935885;C:282462046;G:322914710;T:286516924;N:518185	50		312935885	282462046	322914710	286516924	518185	SRX2480052	SRS1910956	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00262		0.00033		0.99764		0.69195		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
41784	41784	SRR5162097	SRX2480051	SRS1910955	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					PLC5shS6K1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:PLC5shS6K1\|BioSampleModel:Model organism or animal	PLC5shS6K1	PLC5shS6K1	PLC5shS6K1	1			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1205157400.0	24103148.0	CL100006841 L02 25 1.fq.gz	0:50	A:305738728;C:286350102;G:329378158;T:283136091;N:554321	50		305738728	286350102	329378158	283136091	554321	SRX2480051	SRS1910955	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00275		0.00036		0.99801		0.66666		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
41785	41785	SRR5162096	SRX2480050	SRS1910954	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					HepG2shS6K1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:HepG2shS6K1\|BioSampleModel:Model organism or animal	HepG2shS6K1	HepG2shS6K1	HepG2shS6K1	Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1203548150.0	24070963.0	CL100006841 L02 23 1.fq.gz	0:50	A:307598832;C:285812241;G:331356323;T:278082314;N:698440	50		307598832	285812241	331356323	278082314	698440	SRX2480050	SRS1910954	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00192		0.00012		0.99784		0.60818		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
41786	41786	SRR5162095	SRX2480049	SRS1910953	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					Hep3BshCtrl1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:Hep3BshCtrl1\|BioSampleModel:Model organism or animal	Hep3BshCtrl1	Hep3BshCtrl1	Hep3BshCtrl1	Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1201618100.0	24032362.0	CL100006841 L02 20 1.fq.gz	0:50	A:301938424;C:291014141;G:326734280;T:281455564;N:475691	50		301938424	291014141	326734280	281455564	475691	SRX2480049	SRS1910953	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00522		0.00084		0.99722		0.61317		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
41787	41787	SRR5162094	SRX2480048	SRS1910952	SRP096313	PRJNA360680	S6K1 project raw sequence reads	PRJNA360680	Other					HepG2shCtrl1		breed:not applicable\|strain:not applicable\|age:6 dpf provider:not applicable\|sex:not collected\|tissue:embryro\|treatment:HepG2shCtrl1\|BioSampleModel:Model organism or animal	HepG2shCtrl1	HepG2shCtrl1	HepG2shCtrl1	Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	COMPLETE_GENOMICS	Complete Genomics		SRP096313					1205042850.0	24100857.0	CL100006841 L02 22 1.fq.gz	0:50	A:310292006;C:282567913;G:329631833;T:282050651;N:500447	50		310292006	282567913	329631833	282050651	500447	SRX2480048	SRS1910952	SRA525651	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong\|School of Life Sciences	1	0.00164		0.00012		0.99784		0.62847		50		T		under 1.2% mapping rate	legacy	early	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-01-10	Larval	Larval	Embryo Imprecise	All anatomical structures
42301	42301	SRR5579865	SRX2837982	SRS2212147	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					1207 2		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 2\|BioSampleModel:Model organism or animal	2002 2	1207 2 S1 L001	1207 2 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1531873131.0	5203504.0	1207 2 S2 L001 2 paired.fq.gz	0:148.34 1:146.06	A:384469512;C:380138079;G:381661689;T:385603823;N:28	148	146	384469512	380138079	381661689	385603823	28	SRX2837982	SRS2212147	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97313	0.97391	0.03931	0.03966	0.73675	0.74186	0.47243	0.47819	151	150	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42302	42302	SRR5579866	SRX2837981	SRS2212146	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					1207 1		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 1\|BioSampleModel:Model organism or animal	2002 1	1207 1 S1 L001	1207 1 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1250178633.0	4243308.0	1207 1 S1 L001 2 paired.fq.gz	0:148.83 1:145.79	A:314820390;C:308887372;G:310674271;T:315796566;N:34	148	145	314820390	308887372	310674271	315796566	34	SRX2837981	SRS2212146	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97174	0.9719	0.04506	0.04505	0.73154	0.73683	0.4817	0.48252	150	148	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42303	42303	SRR5579867	SRX2837980	SRS2212145	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					AB 1		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB1\|BioSampleModel:Model organism or animal	WT1	AB1 S1 L001	AB1 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1819768909.0	6190653.0	AB1 S1 L001 2 paired.fq.gz	0:148.08 1:145.88	A:465877977;C:442905762;G:444673127;T:466312043;N:0	148	145	465877977	442905762	444673127	466312043	0	SRX2837980	SRS2212145	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97169	0.97078	0.03527	0.03575	0.72823	0.73338	0.48283	0.48226	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42304	42304	SRR5579868	SRX2837979	SRS2212143	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					1207 3		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:1207 3\|BioSampleModel:Model organism or animal	2002 3	1207 3 S1 L001	1207 3 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1045991851.0	3554741.0	1207 3 S3 L001 2 paired.fq.gz	0:148.38 1:145.87	A:263998819;C:257909132;G:259440555;T:264643331;N:14	148	145	263998819	257909132	259440555	264643331	14	SRX2837979	SRS2212143	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97252	0.97273	0.0409	0.04037	0.74213	0.74574	0.48248	0.48634	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42305	42305	SRR5579869	SRX2837978	SRS2212142	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					AB 3		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB3\|BioSampleModel:Model organism or animal	WT3	AB3 S1 L001	AB3 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1126218531.0	3826972.0	AB3 S3 L001 1 paired.fq.gz	0:148.46 1:145.83	A:285650942;C:276774884;G:276765238;T:287027467;N:0	148	145	285650942	276774884	276765238	287027467	0	SRX2837978	SRS2212142	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97355	0.97389	0.03977	0.04012	0.71999	0.72506	0.47576	0.4728	149	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
42306	42306	SRR5579870	SRX2837977	SRS2212144	SRP107584	PRJNA387320	Danio rerio 1207 Raw sequence reads	PRJNA387320	Other					AB 2		breed:not applicable\|strain:not applicable\|age:1 month\|biomaterial provider:not applicable\|sex:not collected\|tissue:Embyro\|treatment:AB2\|BioSampleModel:Model organism or animal	WT2	AB2 S1 L001	AB2 S1 L001	The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina MiSeq		SRP107584					1716453669.0	5815815.0	AB2 S2 L001 1 paired.fq.gz	0:148.63 1:146.50	A:430519895;C:426826400;G:426635292;T:432472082;N:0	148	146	430519895	426826400	426635292	432472082	0	SRX2837977	SRS2212144	SRA563090	The Chinese University of Hong Kong\|School of Life Sciences	The Chinese University of Hong Kong	2	0.97735	0.97725	0.02854	0.02833	0.73196	0.73484	0.48256	0.4861	151	151	B	B	biological fallback assumption	illumina	miseq	unknown	random_priming	unknown	bulk	unknown	unknown	China	2017-05-20	Juvenile	Juvenile	Embryo Imprecise	All anatomical structures
52242	52242	SRR9047069	SRX5823596	SRS4751717	SRP198207	PRJNA542583	Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation	PRJNA542583	Other	Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.			stdMO PBS	stdMO PBS		strain:Tu\|isolate:primary cell\|dev stage:gastrulation\|sex:not determined\|tissue:embryo\|collection date:2016 11 13\|genotype:wild type\|geo loc name:China: Beijing\|sample type:embryos\|BioSampleModel:Model organism or animal	tspan RNA seq	uniprot	uniprot	RNA seq			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	BGISEQ	BGISEQ-500		SRP198207			161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz	fastq	633650654.0	12931646.0	161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz	0:49 1:0	A:165787428;C:152969494;G:145599180;T:169168973;N:125579	49	0	165787428	152969494	145599180	169168973	125579	SRX5823596	SRS4751717	SRA885639	Tsinghua University\|School of Life Sciences	Tsinghua University	1	0.93004		0.09559		0.753		0.47488		49		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-05-30	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
55447	55447	SRR10436022	SRX7131796	SRS5640788	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				2bp 120hpf		strain:rnf213a mutant\|dev stage:120hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 8	rnf213a 8	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_8	fastq	4982904300.0	33219362.0	rnf213a 8.gz	0:0 1:150	A:1324339848;C:1163795168;G:1165190242;T:1329576411;N:2631	0	150	1324339848	1163795168	1165190242	1329576411	2631	SRX7131796	SRS5640788	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.92735		0.08973		0.66523		0.48455		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55448	55448	SRR10436027	SRX7131795	SRS5640788	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				2bp 120hpf		strain:rnf213a mutant\|dev stage:120hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 7	rnf213a 7	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_7	fastq	4982904300.0	33219362.0	rnf213a 7.gz	0:150 1:0	A:1334481379;C:1157336743;G:1153222575;T:1337750420;N:113183	150	0	1334481379	1157336743	1153222575	1337750420	113183	SRX7131795	SRS5640788	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.92697		0.08859		0.6522		0.47736		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55449	55449	SRR10436023	SRX7131794	SRS5640787	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				normal 120hpf		strain:wild type\|dev stage:120hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 6	rnf213a 6	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_6	fastq	4604017500.0	30693450.0	rnf213a 6.gz	0:0 1:150	A:1223063228;C:1075059595;G:1073833007;T:1232058851;N:2819	0	150	1223063228	1075059595	1073833007	1232058851	2819	SRX7131794	SRS5640787	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.9235		0.09498		0.66827		0.47851		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55450	55450	SRR10436026	SRX7131793	SRS5640787	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				normal 120hpf		strain:wild type\|dev stage:120hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 5	rnf213a 5	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_5	fastq	4604017500.0	30693450.0	rnf213a 5.gz	0:150 1:0	A:1233642245;C:1066547157;G:1063728944;T:1239996010;N:103144	150	0	1233642245	1066547157	1063728944	1239996010	103144	SRX7131793	SRS5640787	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.9238		0.09388		0.6549		0.4787		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55451	55451	SRR10436024	SRX7131792	SRS5640786	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				2bp 72hpf		strain:rnf213a mutant\|dev stage:72hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 4	rnf213a 4	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_4	fastq	3640003350.0	24266689.0	rnf213a 4.gz	0:0 1:150	A:957485805;C:856078896;G:866344396;T:959578628;N:515625	0	150	957485805	856078896	866344396	959578628	515625	SRX7131792	SRS5640786	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.93507		0.08252		0.67186		0.4731		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55452	55452	SRR10436025	SRX7131791	SRS5640786	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				2bp 72hpf		strain:rnf213a mutant\|dev stage:72hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 3	rnf213a 3	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_3	fastq	3640003350.0	24266689.0	rnf213a 3.gz	0:150 1:0	A:959700410;C:857785674;G:859574997;T:962707972;N:234297	150	0	959700410	857785674	859574997	962707972	234297	SRX7131791	SRS5640786	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.93504		0.08216		0.66541		0.4721		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55453	55453	SRR10436028	SRX7131790	SRS5640785	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				normal 72hpf		strain:wild type\|dev stage:72hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 2	rnf213a 2	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_2	fastq	3592044900.0	23946966.0	rnf213a 2.gz	0:0 1:150	A:950382154;C:839432686;G:850391648;T:951328573;N:509839	0	150	950382154	839432686	850391648	951328573	509839	SRX7131790	SRS5640785	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.93222		0.09138		0.66087		0.48076		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures
55454	55454	SRR10436029	SRX7131789	SRS5640785	SRP229649	PRJNA588137	rnf213a knockout zebrafish Transcriptome or Gene expression	PRJNA588137	Transcriptome Analysis	To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf.				normal 72hpf		strain:wild type\|dev stage:72hpf\|sex:pooled male and female\|tissue:whole mount embryos\|BioSampleModel:Model organism or animal	RNA Seq of Danio rerio: whole mount embryos	rnf213a 1	rnf213a 1	The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	HiSeq X Ten		SRP229649			rnf213a_1	fastq	3592044900.0	23946966.0	rnf213a 1.gz	0:150 1:0	A:952165099;C:842448366;G:843305876;T:953891694;N:233865	150	0	952165099	842448366	843305876	953891694	233865	SRX7131789	SRS5640785	SRA993760	First affiliated hospital of Sun Yat-sen university\|neurology	First affiliated hospital of Sun Yat-sen university	1	0.93128		0.09035		0.65445		0.47792		150		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown	China	2019-11-13	Larval	Larval	Embryo Imprecise	All anatomical structures

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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");;