rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.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.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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
9825,ERR2102841,ERX2160152,ERS1883528,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N3 nabu RNA,SAMEA104224510,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N3 nabu RNA s,N3 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N3_R1_all.fastq.gz,fastq,1410139550.0,18670564.0,E MTAB 5992:N3 nabu RNA,0:75.53 1:0,A:353294009;C:340727934;G:322476371;T:393200193;N:441043,75,0,,,353294009,340727934,322476371,393200193,441043,ERX2160152,ERS1883528,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95434,,0.08906,,0.66935,,0.47788,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9826,ERR2102840,ERX2160151,ERS1883527,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N2 nabu RNA,SAMEA104224509,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N2 nabu RNA s,N2 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N2_R1_all.fastq.gz,fastq,1478621168.0,19576865.0,E MTAB 5992:N2 nabu RNA,0:75.53 1:0,A:369453299;C:359092235;G:341176884;T:408389810;N:508940,75,0,,,369453299,359092235,341176884,408389810,508940,ERX2160151,ERS1883527,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95582,,0.08202,,0.67718,,0.47812,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9827,ERR2102839,ERX2160150,ERS1883526,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,N1 nabu RNA,SAMEA104224508,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:N1 nabu RNA s,N1 nabu RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:NaBu|Experimental Factor: dose:2,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,N1_R1_all.fastq.gz,fastq,1531713181.0,20277882.0,E MTAB 5992:N1 nabu RNA,0:75.54 1:0,A:386600603;C:373317031;G:350339456;T:420938891;N:517200,75,0,,,386600603,373317031,350339456,420938891,517200,ERX2160150,ERS1883526,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.9552,,0.08124,,0.67685,,0.47578,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9828,ERR2102838,ERX2160149,ERS1883525,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C3 control RNA,SAMEA104224507,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C3 control RNA s,C3 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C3_R1_all.fastq.gz,fastq,1380662008.0,18279108.0,E MTAB 5992:C3 control RNA,0:75.53 1:0,A:345997031;C:338444594;G:316575258;T:379195977;N:449148,75,0,,,345997031,338444594,316575258,379195977,449148,ERX2160149,ERS1883525,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95615,,0.08131,,0.68694,,0.45267,,74,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9829,ERR2102837,ERX2160148,ERS1883524,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C2 control RNA,SAMEA104224506,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224506|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C2 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C2 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C2 control RNA s,C2 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C2_R1_all.fastq.gz,fastq,1336640735.0,17695627.0,E MTAB 5992:C2 control RNA,0:75.54 1:0,A:338213530;C:326808990;G:303983789;T:367147896;N:486530,75,0,,,338213530,326808990,303983789,367147896,486530,ERX2160148,ERS1883524,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95427,,0.08628,,0.67706,,0.47245,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
9830,ERR2102836,ERX2160147,ERS1883523,ERP040145,PRJEB37796,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E-MTAB-5992,Transcriptome Analysis,We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours  in order to assess the effect of inhibition of the HDAC pathway in these animals,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992,,Protocols: zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,C1 control RNA,SAMEA104224505,Fundacao Champalimaud,ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224505|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C1 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C1 control RNA|strain:AB,,,,,,,,,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,E MTAB 5992:C1 control RNA s,C1 control RNA s,Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,zebrafish were isolated during pharyngula stage  daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later  and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001,Experimental Factor: compound:PBS,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,ERP040145,Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf,ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16,C1_R1_all.fastq.gz,fastq,1297694845.0,17180544.0,E MTAB 5992:C1 control RNA,0:75.53 1:0,A:322048172;C:316542683;G:299227724;T:359449433;N:426833,75,0,,,322048172,316542683,299227724,359449433,426833,ERX2160147,ERS1883523,ERA1011308,Fundacao Champalimaud|European Nucleotide Archive,Fundacao Champalimaud|European Nucleotide Archive,1,0.95505,,0.08541,,0.67659,,0.48159,,75,,B,,usable mapping rate,illumina,early_illumina,unknown,random_priming,trueseq,bulk,unknown,unknown,,Portugal,2017-08-23,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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 transcription and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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 and second strand synthesis reagents were dispensed using the Nanodrop II GC biotech. post generation of cDNA from the original mRNA  all cells from one plate were pooled and the pooled sample was amplified linearly with in vitro transcription. The amplified RNA was then reverse transcribed to cDNA using a random hexamer primers Hashimshony et al.  2016. To generate sequencing libraries  RPI series index primers were used for library PCR.,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,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,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,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,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,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,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,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,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 manufacturer’s 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,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 manufacturer’s 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,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 manufacturer’s 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,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 manufacturer’s 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,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 manufacturer’s 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,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 manufacturer’s 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
43749,SRR6047139,SRX3194198,SRS2520599,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Control,,strain:AB|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin40ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeAB at 6dpf,Control,Control,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAACRAAPEI-20_L1_2.fq.gz,fastq fastq,6648275100.0,22160917.0,FCHCKWTBBXX WHZEBleaEAACRAAPEI 20 L1 2.fq.gz,0:150 1:150,A:1742296604;C:1590637599;G:1588423459;T:1726207133;N:710305,150,150,,,1742296604,1590637599,1588423459,1726207133,710305,SRX3194198,SRS2520599,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.91275,0.9117,0.06243,0.06238,0.6743,0.68002,0.48294,0.4832,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43750,SRR6047140,SRX3194197,SRS2520598,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Myc,,strain:Tgfabp10a:TetON; TRE:Myc|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin41ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeMyc at 6dpf,Myc,Myc,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAABRAAPEI-19_L1_2.fq.gz,fastq fastq,6562440900.0,21874803.0,FCHCKWTBBXX WHZEBleaEAABRAAPEI 19 L1 2.fq.gz,0:150 1:150,A:1690373636;C:1597720217;G:1597100889;T:1676557094;N:689064,150,150,,,1690373636,1597720217,1597100889,1676557094,689064,SRX3194197,SRS2520598,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.9112,0.9098,0.05364,0.05314,0.68199,0.68826,0.47506,0.48785,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43751,SRR6047141,SRX3194196,SRS2520597,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Kras,,strain:Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin42ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras at 6dpf,Kras,Kras,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAADRAAPEI-21_L1_2.fq.gz,fastq fastq,6567871200.0,21892904.0,FCHCKWTBBXX WHZEBleaEAADRAAPEI 21 L1 2.fq.gz,0:150 1:150,A:1728249052;C:1564137653;G:1559231198;T:1715565790;N:687507,150,150,,,1728249052,1564137653,1559231198,1715565790,687507,SRX3194196,SRS2520597,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.93087,0.92811,0.06342,0.06328,0.66941,0.67493,0.47581,0.47601,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
43752,SRR6047142,SRX3194195,SRS2520596,SRP117794,PRJNA407650,Danio rerio Transcriptome or Gene expression,PRJNA407650,Transcriptome Analysis,We performed RNA sequencing on four groups of zebrafish larvae: control  TgMyc  TgKras  TgMyc&amp;TgKras to analyze the expression of genes involved in the lipid associated pathways.The results revealed high dynamic alterations in almost all aspects of lipid metabolism  among which  the expressions of genes involved in TG/DG/GP transformation and FA desaturation/elongation displayed intensive changes  in consistent with our observations in lipodomics profiling,,,,,Kras&amp;Myc,,strain:Tgfabp10a:TetON; TRE:Myc&Tgfabp10a:TetON; TRE:eGFP krasv12|breed:breed with AB|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not determined|tissue:whole larvae|treatment:E3 with Doxcyclin43ug/ml|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeKras&Myc at 6dpf,Kras&amp;Myc,Kras&Myc,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP117794,,,FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_1.fq.gz FCHCKWTBBXX-WHZEBleaEAAARAAPEI-18_L1_2.fq.gz,fastq fastq,6464892900.0,21549643.0,FCHCKWTBBXX WHZEBleaEAAARAAPEI 18 L1 2.fq.gz,0:150 1:150,A:1676039250;C:1565410813;G:1564742343;T:1658019117;N:681377,150,150,,,1676039250,1565410813,1564742343,1658019117,681377,SRX3194195,SRS2520596,SRA608833,"Fudan University|Department of Biochemistry and Molecular Biology,",Fudan University,2,0.8919,0.88916,0.05486,0.05403,0.67882,0.68505,0.49625,0.49784,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2017-09-17,Larval,Larval,Whole Organism,All anatomical structures
49393,SRR7896793,SRX4734232,SRS3816349,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,homozygous mutant,,strain:tnnt2a / |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of tnnt2a homozygous mutant zebrafish post Dox induction,homozygous mutant,homozygous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,mutant_L1_1.fq.gz mutant_L1_2.fq.gz,fastq fastq,6615980100.0,22053267.0,mutant L1 2.fq.gz,0:150 1:150,A:1714364351;C:1596934293;G:1606676062;T:1697294755;N:710639,150,150,,,1714364351,1596934293,1606676062,1697294755,710639,SRX4734232,SRS3816349,,,Children's hospital of Fudan University,2,0.88229,0.88599,0.05373,0.05345,0.67042,0.67259,0.45764,0.46314,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49394,SRR7896794,SRX4734231,SRS3816348,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,non homozygous mutant,,strain:tnnt2a+/ |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of non tnnt2a homozygous mutant zebrafish post Dox induction,non homozygous mutant,non homozygous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,non mutant_L1_1.fq.gz non mutant_L1_2.fq.gz,fastq fastq,6561723600.0,21872412.0,non mutant L1 2.fq.gz,0:150 1:150,A:1689788269;C:1592764528;G:1601424044;T:1677002898;N:743861,150,150,,,1689788269,1592764528,1601424044,1677002898,743861,SRX4734231,SRS3816348,,,Children's hospital of Fudan University,2,0.8991,0.90343,0.05565,0.05598,0.66752,0.66929,0.4567,0.46188,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49395,SRR7896795,SRX4734230,SRS3816347,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,transgene homozygous mutant,,strain:Tgcmlc2:TetON; tnnt2a p2A mKate2&tnnt2a / |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of transgene tnnt2a homozygous mutant zebrafish post Dox induction,transgene homozygous mutant,transgene homozygous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,transgene mutant_L1_1.fq.gz transgene mutant_L1_2.fq.gz,fastq fastq,6496976700.0,21656589.0,transgene mutant L1 2.fq.gz,,,,,,,,,,,,SRX4734230,SRS3816347,,,Children's hospital of Fudan University,2,0.9041,0.8968,0.06697,0.06595,0.66789,0.66787,0.45258,0.45688,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
49396,SRR7896796,SRX4734229,SRS3816346,SRP162489,PRJNA492836,Danio rerio Transcriptome or Gene expression,PRJNA492836,Transcriptome Analysis,to study the feasibility of gene therapy of TNNT2 mutant related cardiomyopathy,,,,,non transgene homozyous mutant,,strain:Tgcmlc2:TetON; tnnt2a p2A mKate2&tnnt2a+/ |cultivar:not applicable|ecotype:not applicable|age:3 dpf stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of non transgene tnnt2a homozygous mutant zebrafish post Dox induction,non transgene homozyous mutant,non transgene homozyous mutant,In our project  we sequence 4 samples use Illumina Hiseq platform  and on average we generated about 6.56Gb bases from each sample. We also map clean reads to reference genome  on average 71.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP162489,,,transgene non mutant_L1_1.fq.gz transgene non mutant_L1_2.fq.gz,fastq fastq,6541491300.0,21804971.0,transgene non mutant L1 1.fq.gz,0:150 1:150,A:1689774214;C:1582775230;G:1591564227;T:1676650852;N:726777,150,150,,,1689774214,1582775230,1591564227,1676650852,726777,SRX4734229,SRS3816346,,,Children's hospital of Fudan University,2,0.89333,0.89894,0.05656,0.05595,0.66665,0.66888,0.46433,0.46204,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-24,Larval,Larval,Whole Organism,All anatomical structures
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,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,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,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,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,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,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,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,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
58554,SRR11362969,SRX7964365,SRS6350268,SRP253564,PRJNA613729,Danio rerio Transcriptome or Gene expression,PRJNA613729,Transcriptome Analysis,Transcriptome of serpini1 deficient zebrafish by CRISPR/Cas9 technique and an inducible neuroserpin overexpression model under the Huc promoter in the zebrafish,,,,Model organism or animal sample from Danio rerio,Tgserpini1,,strain:Tg huc: teton: gal4; tre: serpini1: mkate2|age:7dpf|dev stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeTgserpini1 at 7dpf,Tgserpini1,Tgserpini1,In our project  we sequence 3 samples use Illumina Hiseq platform  and on average we generated about 6.68Gb bases from each sample. We also map clean reads to reference genome  on average 79.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253564,,,FCHGNGYCCXY_L3_WHZEBozrEAACRAAPEI-17_1.fq.gz FCHGNGYCCXY_L3_WHZEBozrEAACRAAPEI-17_2.fq.gz,fastq fastq,6640137000.0,22133790.0,FCHGNGYCCXY L3 WHZEBozrEAACRAAPEI 17 1.fq.gz,0:150 1:150,A:1729320460;C:1602342446;G:1594872338;T:1713455542;N:146214,150,150,,,1729320460,1602342446,1594872338,1713455542,146214,SRX7964365,SRS6350268,SRA1057721,"Huashan Hospital, Fudan University|Department of Neurology","Huashan Hospital, Fudan University",2,0.90809,0.90905,0.05765,0.05783,0.67026,0.67399,0.46996,0.47114,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-21,Larval,Larval,Whole Organism,All anatomical structures
58555,SRR11362970,SRX7964364,SRS6350267,SRP253564,PRJNA613729,Danio rerio Transcriptome or Gene expression,PRJNA613729,Transcriptome Analysis,Transcriptome of serpini1 deficient zebrafish by CRISPR/Cas9 technique and an inducible neuroserpin overexpression model under the Huc promoter in the zebrafish,,,,Model organism or animal sample from Danio rerio,serpini1 / ,,strain:Tgserpini1 / |age:7dpf|dev stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaeserpini1 /  at 7dpf,serpini1 / ,serpini1 / ,In our project  we sequence 3 samples use Illumina Hiseq platform  and on average we generated about 6.68Gb bases from each sample. We also map clean reads to reference genome  on average 79.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253564,,,FCHGNGYCCXY_L3_WHZEBozrEAABRAAPEI-16_2.fq.gz FCHGNGYCCXY_L3_WHZEBozrEAABRAAPEI-16_1.fq.gz,fastq fastq,6617653200.0,22058844.0,FCHGNGYCCXY L3 WHZEBozrEAABRAAPEI 16 1.fq.gz,0:150 1:150,A:1716574905;C:1602024658;G:1595975688;T:1702935179;N:142770,150,150,,,1716574905,1602024658,1595975688,1702935179,142770,SRX7964364,SRS6350267,SRA1057721,"Huashan Hospital, Fudan University|Department of Neurology","Huashan Hospital, Fudan University",2,0.90372,0.90544,0.06479,0.06578,0.67696,0.68045,0.45687,0.46187,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-21,Larval,Larval,Whole Organism,All anatomical structures
58556,SRR11362971,SRX7964363,SRS6350266,SRP253564,PRJNA613729,Danio rerio Transcriptome or Gene expression,PRJNA613729,Transcriptome Analysis,Transcriptome of serpini1 deficient zebrafish by CRISPR/Cas9 technique and an inducible neuroserpin overexpression model under the Huc promoter in the zebrafish,,,,Model organism or animal sample from Danio rerio,control,,strain:AB|age:7dpf|dev stage:larval|sex:pooled male and female|tissue:whole larvae|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish larvaecontrol at 7dpf,control,control,In our project  we sequence 3 samples use Illumina Hiseq platform  and on average we generated about 6.68Gb bases from each sample. We also map clean reads to reference genome  on average 79.49% reads are mapped,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP253564,,,FCHGNGYCCXY_L3_WHZEBozrEAAARAAPEI-168_1.fq.gz FCHGNGYCCXY_L3_WHZEBozrEAAARAAPEI-168_2.fq.gz,fastq fastq,6741448200.0,22471494.0,FCHGNGYCCXY L3 WHZEBozrEAAARAAPEI 168 1.fq.gz,0:150 1:150,A:1758797585;C:1622874542;G:1617573676;T:1742064320;N:138077,150,150,,,1758797585,1622874542,1617573676,1742064320,138077,SRX7964363,SRS6350266,SRA1057721,"Huashan Hospital, Fudan University|Department of Neurology","Huashan Hospital, Fudan University",2,0.89722,0.89787,0.06821,0.06852,0.67675,0.68256,0.45822,0.46023,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-21,Larval,Larval,Whole Organism,All anatomical structures
72445,SRR22540104,SRX18504097,SRS15974727,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Treatment 3,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,T3/,T3/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,T3.AddRG.Reorder.Sort.bam,bam,4395695600.0,21978478.0,T3.AddRG.Reorder.Sort.bam,0:100 1:100,A:1142519361;C:1049796532;G:1054171464;T:1149208243;N:0,100,100,,,1142519361,1049796532,1054171464,1149208243,0,SRX18504097,SRS15974727,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.95843,0.96189,0.05928,0.05837,0.66996,0.67022,0.48134,0.48129,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72446,SRR22540105,SRX18504096,SRS15974726,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Treatment 2,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,T2/,T2/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,T2.AddRG.Reorder.Sort.bam,bam,4614912600.0,23074563.0,T2.AddRG.Reorder.Sort.bam,0:100 1:100,A:1188643000;C:1115164590;G:1120634369;T:1190470641;N:0,100,100,,,1188643000,1115164590,1120634369,1190470641,0,SRX18504096,SRS15974726,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.95664,0.96166,0.05002,0.04822,0.68635,0.68554,0.47517,0.46481,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72447,SRR22540106,SRX18504095,SRS15974725,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Treatment 1,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,T1/,T1/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,T1.AddRG.Reorder.Sort.bam,bam,4621886200.0,23109431.0,T1.AddRG.Reorder.Sort.bam,0:100 1:100,A:1193465655;C:1112344935;G:1119903386;T:1196172224;N:0,100,100,,,1193465655,1112344935,1119903386,1196172224,0,SRX18504095,SRS15974725,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.95679,0.96088,0.05344,0.05139,0.67754,0.67598,0.462,0.46124,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72448,SRR22540107,SRX18504094,SRS15974724,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Control 3,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C3/,C3/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,C3.AddRG.Reorder.Sort.bam,bam,4617709400.0,23088547.0,C3.AddRG.Reorder.Sort.bam,0:100 1:100,A:1198527314;C:1106175441;G:1112503633;T:1200503012;N:0,100,100,,,1198527314,1106175441,1112503633,1200503012,0,SRX18504094,SRS15974724,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.95798,0.96137,0.05412,0.05264,0.67223,0.67048,0.46376,0.46409,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72449,SRR22540108,SRX18504093,SRS15974723,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Control 2,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C2/,C2/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,C2.AddRG.Reorder.Sort.bam,bam,4871905600.0,24359528.0,C2.AddRG.Reorder.Sort.bam,0:100 1:100,A:1257717743;C:1172780375;G:1176887548;T:1264519934;N:0,100,100,,,1257717743,1172780375,1176887548,1264519934,0,SRX18504093,SRS15974723,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.96005,0.96318,0.05702,0.05549,0.66789,0.66697,0.47093,0.46583,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72450,SRR22540109,SRX18504092,SRS15974722,SRP411489,PRJNA908883,Zebrafish PFHxS exposure RNA seq,PRJNA908883,Other,RAN seq of zebrafish embryos post 5 days PFHxS exposure,,,,Model organism or animal sample from Danio rerio,Control 1,,strain:AB|dev stage:5dpf|sex:not determined|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C1/,C1/,effect of pfhxs,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP411489,,,C1.AddRG.Reorder.Sort.bam,bam,4632466800.0,23162334.0,C1.AddRG.Reorder.Sort.bam,0:100 1:100,A:1194920249;C:1116526905;G:1121202833;T:1199816813;N:0,100,100,,,1194920249,1116526905,1121202833,1199816813,0,SRX18504092,SRS15974722,SRA1553988,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.95802,0.96207,0.05444,0.05319,0.67371,0.67247,0.47155,0.46736,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-05,Larval,Larval,Whole Organism,All anatomical structures
72614,SRR22891482,SRX18849297,SRS16280582,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Mutant3,,strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,S3,S3,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,S3.AddRG.Reorder.Sort.bam,bam,4571163800.0,22855819.0,S3.AddRG.Reorder.Sort.bam,0:100 1:100,A:1194682262;C:1085195756;G:1103429751;T:1187856031;N:0,100,100,,,1194682262,1085195756,1103429751,1187856031,0,SRX18849297,SRS16280582,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.93076,0.93744,0.0661,0.06566,0.67825,0.67675,0.46849,0.46581,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures
72615,SRR22891483,SRX18849296,SRS16280581,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Mutant2,,strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,S2,S2,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,S2.AddRG.Reorder.Sort.bam,bam,4600792600.0,23003963.0,S2.AddRG.Reorder.Sort.bam,0:100 1:100,A:1200126269;C:1095166595;G:1110394784;T:1195104952;N:0,100,100,,,1200126269,1095166595,1110394784,1195104952,0,SRX18849296,SRS16280581,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.93762,0.94385,0.06417,0.06338,0.67288,0.67282,0.46354,0.46465,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures
72616,SRR22891484,SRX18849295,SRS16280580,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Mutant1,,strain:sf3b4|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,S1,S1,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,S1.AddRG.Reorder.Sort.bam,bam,4597426600.0,22987133.0,S1.AddRG.Reorder.Sort.bam,0:100 1:100,A:1198474483;C:1095576259;G:1111544092;T:1191831766;N:0,100,100,,,1198474483,1095576259,1111544092,1191831766,0,SRX18849295,SRS16280580,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.93381,0.93956,0.06594,0.06432,0.67529,0.67225,0.46816,0.46785,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures
72617,SRR22891485,SRX18849294,SRS16280579,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Control3,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C3,C3,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,C3.AddRG.Reorder.Sort.bam,bam,4604458600.0,23022293.0,C3.AddRG.Reorder.Sort.bam,0:100 1:100,A:1212479855;C:1086425627;G:1078320217;T:1227232901;N:0,100,100,,,1212479855,1086425627,1078320217,1227232901,0,SRX18849294,SRS16280579,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.9375,0.94189,0.06929,0.06838,0.68097,0.68032,0.46981,0.46746,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures
72618,SRR22891486,SRX18849293,SRS16280578,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Control2,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C2,C2,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,C2.AddRG.Reorder.Sort.bam,bam,4518373800.0,22591869.0,C2.AddRG.Reorder.Sort.bam,0:100 1:100,A:1177788565;C:1076096675;G:1084632400;T:1179856160;N:0,100,100,,,1177788565,1076096675,1084632400,1179856160,0,SRX18849293,SRS16280578,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.93712,0.94281,0.05459,0.05451,0.67669,0.67543,0.46485,0.46607,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures
72619,SRR22891487,SRX18849292,SRS16280577,SRP414808,PRJNA915212,Danio rerio strain: 5dpf AB and sf3b4 /  Raw sequence reads,PRJNA915212,Whole Genome Sequencing,A project that using 5dpf AB control and sf3b4 /  mutant for RNA sequencing,,,,Model organism or animal sample from Danio rerio,Control1,,strain:AB|dev stage:5dpf|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish embryo,C1,C1,RNA seq of 5dpf,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP414808,,assembly:GRCz11,C1.AddRG.Reorder.Sort.bam,bam,4546744400.0,22733722.0,C1.AddRG.Reorder.Sort.bam,0:100 1:100,A:1170343546;C:1097144275;G:1111316933;T:1167939646;N:0,100,100,,,1170343546,1097144275,1111316933,1167939646,0,SRX18849292,SRS16280577,SRA1565404,Dr. William TSE/ Kyushu University|Faculty of Agriculture,Dr. William TSE/ Kyushu University,2,0.94204,0.94786,0.05052,0.04964,0.68227,0.68097,0.46172,0.45485,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2022-12-26,Larval,Larval,Whole Organism,All anatomical structures