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323 rows where experiment.library_selection = "RANDOM" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation >10

devstage_curation_coarse 6

experiment.platform 4

technology 3

tissue_curation 2

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

  • All anatomical structures · 323 ✖

experiment.library_selection 1

  • RANDOM · 323 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.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 8088 ERR034127 ERX012653 ERS032268 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 50% epiboly stage zebrafish embryo 50 epiboly SAMEA791629 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 50epiboly JKE Drerio rna seq Transcriptome profiling of 50% epiboly stages of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz SOLiD_native SOLiD_native 3929903550.0 78598071.0 KI BN JKE DRERIO RNASEQ 2011 50epiboly 0:50   50                 ERX012653 ERS032268 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.60757   0.09893   0.94899   0.77821   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Gastrula Embryo Embryo Imprecise All anatomical structures
8089 8089 ERR034126 ERX012652 ERS032267 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 512 cell stage zebrafish embryo 512 cell SAMEA791632 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 512cell JKE Drerio rna seq Transcriptome profiling of 512 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz SOLiD_native SOLiD_native 3918756250.0 78375125.0 KI BN JKE DRERIO RNASEQ 2011 512cell 0:50   50                 ERX012652 ERS032267 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.63824   0.09111   0.91969   0.73496   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Blastula Embryo Embryo Imprecise All anatomical structures
8090 8090 ERR034125 ERX012651 ERS032266 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 16 cell stage zebrafish embryo 16 cell SAMEA791631 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 16cell JKE Drerio rna seq Transcriptome profiling of 16 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz SOLiD_native SOLiD_native 4256756500.0 85135130.0 KI BN JKE DRERIO RNASEQ 2011 16cell 0:50   50                 ERX012651 ERS032266 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.57946   0.08115   0.91896   0.72164   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Cleavage Embryo Embryo Imprecise All anatomical structures
8091 8091 ERR034124 ERX012650 ERS032265 ERP000635 PRJEB2512 The Zebrafish transcriptome during early development KI-BN-JKE-DRERIO-RNASEQ-2011 Transcriptome Analysis Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.     RNA extracted from zebrafish embryo at 1 cell stage zebrafish embryo 1 cell SAMEA791630 Department of Biosciences and Nutrition, Karolinska Institutet, Sweden ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen                 Transcriptome profiling of early zebrafish development KI BN JKE DRERIO RNASEQ 2011 1cell JKE Drerio rna seq Transcriptome profiling of 1 cell stage of zebrafish embryos. Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.   RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000635 AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz SOLiD_native SOLiD_native 3676380950.0 73527619.0 KI BN JKE DRERIO RNASEQ 2011 1cell 0:50   50                 ERX012650 ERS032265 ERA029959 KI-BN|Department of Biosciences and Nutrition Department of Biosciences and Nutrition, Karolinska Institutet, Sweden 1 0.64855   0.08432   0.9052   0.74223   50   B   usable mapping rate legacy early unknown random_priming unknown bulk unknown unknown   Sweden 2011-06-09 Zygote Embryo Embryo Imprecise All anatomical structures
9367 9367 ERR145653 ERX121572 ERS151242 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW3 F M pooled fish SAMEA1487368 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW3 B seq WW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW3_B_1.fq.gz WW3_B_2.fq.gz fastq fastq 4347695086.0 21523243.0 E MTAB 1155:WW3 B 0:101 1:101 A:1074237454;C:1092333862;G:1102729864;T:1065390007;N:13003899 101 101     1074237454 1092333862 1102729864 1065390007 13003899 ERX121572 ERS151242 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95796 0.9583 0.02413 0.02313 0.83946 0.8338 0.51717 0.51633 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9368 9368 ERR145654 ERX121560 ERS151233 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW4 F M pooled fish SAMEA1487359 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW4 A seq WW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW4_A_1.fq.gz WW4_A_2.fq.gz fastq fastq 80948470.0 400735.0 E MTAB 1155:WW4 A 0:101 1:101 A:21174054;C:19268727;G:19622428;T:20880804;N:2457 101 101     21174054 19268727 19622428 20880804 2457 ERX121560 ERS151233 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93674 0.92652 0.0383 0.03971 0.84776 0.86028 0.52028 0.51601 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9369 9369 ERR145639 ERX121583 ERS151247 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW4 F M pooled fish SAMEA1487357 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487357|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW4 seq CW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW4_1.fq.gz CW4_2.fq.gz fastq fastq 7322391324.0 36249462.0 E MTAB 1155:CW4 0:101 1:101 A:1915177797;C:1750141576;G:1768328049;T:1887892000;N:851902 101 101     1915177797 1750141576 1768328049 1887892000 851902 ERX121583 ERS151247 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94177 0.93855 0.04669 0.04835 0.81227 0.81663 0.5297 0.53381 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9370 9370 ERR145632 ERX121582 ERS151246 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH2 F M pooled fish SAMEA1487358 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487358|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH2 seq CH2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH2_1.fq.gz CH2_2.fq.gz fastq fastq 6008384960.0 29744480.0 E MTAB 1155:CH2 0:101 1:101 A:1551084475;C:1456651824;G:1467972620;T:1531930144;N:745897 101 101     1551084475 1456651824 1467972620 1531930144 745897 ERX121582 ERS151246 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94484 0.94325 0.04187 0.04238 0.81448 0.8172 0.46639 0.50253 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9371 9371 ERR145634 ERX121581 ERS151245 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH4 F M pooled fish SAMEA1487361 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487361|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH4 seq CH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH4_1.fq.gz CH4_2.fq.gz fastq fastq 5647385104.0 27957352.0 E MTAB 1155:CH4 0:101 1:101 A:1469982057;C:1356659164;G:1371916498;T:1448143269;N:684116 101 101     1469982057 1356659164 1371916498 1448143269 684116 ERX121581 ERS151245 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93865 0.93633 0.0439 0.04446 0.80549 0.80864 0.53045 0.51098 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9372 9372 ERR145651 ERX121579 ERS151239 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW2 F M pooled fish SAMEA1487360 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW2 B seq WW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW2_B_1.fq.gz WW2_B_2.fq.gz fastq fastq 4738967672.0 23460236.0 E MTAB 1155:WW2 B 0:101 1:101 A:1175576318;C:1183749238;G:1198839519;T:1166587116;N:14215481 101 101     1175576318 1183749238 1198839519 1166587116 14215481 ERX121579 ERS151239 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95497 0.95617 0.02438 0.0233 0.82909 0.82455 0.51164 0.51189 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9373 9373 ERR145652 ERX121578 ERS151242 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW3 F M pooled fish SAMEA1487368 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T16:01:13Z|External Id:SAMEA1487368|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T16:01:13Z|INSDC status:public|Submitter Id:E MTAB 1155:WW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW3 A seq WW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW3_A_1.fq.gz WW3_A_2.fq.gz fastq fastq 229808532.0 1137666.0 E MTAB 1155:WW3 A 0:101 1:101 A:59360822;C:55502890;G:56337453;T:58600433;N:6934 101 101     59360822 55502890 56337453 58600433 6934 ERX121578 ERS151242 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93623 0.92715 0.03151 0.03268 0.83735 0.84952 0.52265 0.5038 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9374 9374 ERR145649 ERX121577 ERS151234 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW1 F M pooled fish SAMEA1487370 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW1 B seq WW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW1_B_1.fq.gz WW1_B_2.fq.gz fastq fastq 7635373356.0 37798878.0 E MTAB 1155:WW1 B 0:101 1:101 A:1902965653;C:1900547622;G:1920575326;T:1888470954;N:22813801 101 101     1902965653 1900547622 1920575326 1888470954 22813801 ERX121577 ERS151234 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95977 0.95988 0.02636 0.02563 0.84279 0.83808 0.52131 0.45646 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9375 9375 ERR145636 ERX121576 ERS151244 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW2 F M pooled fish SAMEA1487364 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487364|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:CW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW2 seq CW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW2_1.fq.gz CW2_2.fq.gz fastq fastq 7748012798.0 38356499.0 E MTAB 1155:CW2 0:101 1:101 A:2015650126;C:1864022271;G:1874527501;T:1992894699;N:918201 101 101     2015650126 1864022271 1874527501 1992894699 918201 ERX121576 ERS151244 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94537 0.94243 0.04249 0.04301 0.82213 0.82552 0.52811 0.53747 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9376 9376 ERR145646 ERX121571 ERS151241 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH4 F M pooled fish SAMEA1487367 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH4 A seq WH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH4_A_1.fq.gz WH4_A_2.fq.gz fastq fastq 812883148.0 4024174.0 E MTAB 1155:WH4 A 0:101 1:101 A:209997189;C:196285019;G:198925947;T:207278009;N:396984 101 101     209997189 196285019 198925947 207278009 396984 ERX121571 ERS151241 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94663 0.91942 0.03602 0.03591 0.8424 0.85462 0.51702 0.51147 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9377 9377 ERR145647 ERX121570 ERS151241 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH4 F M pooled fish SAMEA1487367 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487367|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH4 B seq WH4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH4_B_1.fq.gz WH4_B_2.fq.gz fastq fastq 10768144694.0 53307647.0 E MTAB 1155:WH4 B 0:101 1:101 A:2682817583;C:2706807352;G:2714533015;T:2652309644;N:11677100 101 101     2682817583 2706807352 2714533015 2652309644 11677100 ERX121570 ERS151241 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.95867 0.96056 0.02378 0.02413 0.83609 0.83889 0.43331 0.44066 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9378 9378 ERR145655 ERX121569 ERS151233 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW4 F M pooled fish SAMEA1487359 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487359|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW4 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW4 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW4 B seq WW4 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW4_B_1.fq.gz WW4_B_2.fq.gz fastq fastq 6455936968.0 31960084.0 E MTAB 1155:WW4 B 0:101 1:101 A:1610738878;C:1605252294;G:1623372987;T:1597311219;N:19261590 101 101     1610738878 1605252294 1623372987 1597311219 19261590 ERX121569 ERS151233 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.96085 0.96101 0.02863 0.02731 0.84995 0.8452 0.52157 0.51189 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9379 9379 ERR145633 ERX121568 ERS151240 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH3 F M pooled fish SAMEA1487363 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487363|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH3 seq CH3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH3_1.fq.gz CH3_2.fq.gz fastq fastq 6146419640.0 30427820.0 E MTAB 1155:CH3 0:101 1:101 A:1596666196;C:1479913350;G:1493612614;T:1575480940;N:746540 101 101     1596666196 1479913350 1493612614 1575480940 746540 ERX121568 ERS151240 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93901 0.93723 0.04362 0.04417 0.79715 0.7977 0.51473 0.52412 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9380 9380 ERR145650 ERX121567 ERS151239 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW2 F M pooled fish SAMEA1487360 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487360|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW2 A seq WW2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW2_A_1.fq.gz WW2_A_2.fq.gz fastq fastq 280038054.0 1386327.0 E MTAB 1155:WW2 A 0:101 1:101 A:72831492;C:67021049;G:68232991;T:71942949;N:9573 101 101     72831492 67021049 68232991 71942949 9573 ERX121567 ERS151239 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93032 0.9187 0.03207 0.03356 0.82852 0.84139 0.52376 0.52436 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9381 9381 ERR145637 ERX121565 ERS151232 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW3 F M pooled fish SAMEA1487355 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW3 A seq CW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW3_A_1.fq.gz CW3_A_2.fq.gz fastq fastq 2104292580.0 10417290.0 E MTAB 1155:CW3 A 0:101 1:101 A:547829220;C:504948167;G:510803037;T:540521191;N:190965 101 101     547829220 504948167 510803037 540521191 190965 ERX121565 ERS151232 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93423 0.92981 0.04776 0.04835 0.81245 0.81471 0.51349 0.4822 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9382 9382 ERR145631 ERX121564 ERS151237 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CH1 F M pooled fish SAMEA1487356 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487356|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:CH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CH1 seq CH1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CH1_1.fq.gz CH1_2.fq.gz fastq fastq 7734471526.0 38289463.0 E MTAB 1155:CH1 0:101 1:101 A:1980474194;C:1892305985;G:1907192207;T:1953595996;N:903144 101 101     1980474194 1892305985 1907192207 1953595996 903144 ERX121564 ERS151237 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94403 0.94213 0.03862 0.03913 0.82309 0.82556 0.49626 0.49773 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9383 9383 ERR145635 ERX121562 ERS151235 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW1 F M pooled fish SAMEA1487366 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487366|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW1 seq CW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW1_1.fq.gz CW1_2.fq.gz fastq fastq 6202716838.0 30706519.0 E MTAB 1155:CW1 0:101 1:101 A:1612950873;C:1492406749;G:1504306823;T:1592361004;N:691389 101 101     1612950873 1492406749 1504306823 1592361004 691389 ERX121562 ERS151235 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94448 0.94226 0.04304 0.04379 0.81296 0.81489 0.5237 0.52588 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9384 9384 ERR145648 ERX121561 ERS151234 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WW1 F M pooled fish SAMEA1487370 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487370|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WW1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:WW1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WW1 A seq WW1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WW1_A_1.fq.gz WW1_A_2.fq.gz fastq fastq 330954174.0 1638387.0 E MTAB 1155:WW1 A 0:101 1:101 A:86485807;C:78916128;G:80103844;T:85437370;N:11025 101 101     86485807 78916128 80103844 85437370 11025 ERX121561 ERS151234 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.93321 0.92294 0.03445 0.03581 0.84133 0.85267 0.54253 0.53593 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9385 9385 ERR145638 ERX121559 ERS151232 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. CW3 F M pooled fish SAMEA1487355 Genepool AdultAcclimationTemperature:16 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487355|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:CW3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:27 degree C|sample name:E MTAB 1155:CW3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:CW3 B seq CW3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:27 degree C|Experimental Factor: AdultAcclimationTemperature:16 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 CW3_B_1.fq.gz CW3_B_2.fq.gz fastq fastq 6504819756.0 32202078.0 E MTAB 1155:CW3 B 0:101 1:101 A:1653674963;C:1600212014;G:1606437826;T:1637400265;N:7094688 101 101     1653674963 1600212014 1606437826 1637400265 7094688 ERX121559 ERS151232 ERA140546 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94253 0.94443 0.03782 0.03856 0.80661 0.80801 0.49414 0.51667 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9386 9386 ERR147028 ERX122956 ERS151238 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH3 F M pooled fish SAMEA1487362 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487362|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH3 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH3 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH3 seq WH3 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH3_1.fq.gz WH3_2.fq.gz fastq fastq 3197103894.0 15827247.0 E MTAB 1155:WH3 0:101 1:101 A:829020337;C:767623553;G:780642278;T:818288216;N:1529510 101 101     829020337 767623553 780642278 818288216 1529510 ERX122956 ERS151238 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94791 0.91975 0.03726 0.03735 0.84291 0.85622 0.4972 0.50314 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9387 9387 ERR147027 ERX122955 ERS151236 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH2 F M pooled fish SAMEA1487365 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:48:59Z|External Id:SAMEA1487365|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:48:59Z|INSDC status:public|Submitter Id:E MTAB 1155:WH2 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH2 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH2 seq WH2 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH2_1.fq.gz WH2_2.fq.gz fastq fastq 3455989922.0 17108861.0 E MTAB 1155:WH2 0:101 1:101 A:902145358;C:824320050;G:837200815;T:890816825;N:1506874 101 101     902145358 824320050 837200815 890816825 1506874 ERX122955 ERS151236 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94863 0.92001 0.04084 0.04066 0.83796 0.85263 0.5275 0.51735 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9388 9388 ERR147026 ERX122954 ERS151243 ERP001552 PRJEB3112 The effects of temperature on gene expression in zebrafish E-MTAB-1155 Transcriptome Analysis Zebrafish were raised at temperatures of either 27C or 32C as embryos. post hatch fish were raised to maturity at a common control temperature of 27C. Gene expression was measured in the white skeletal muscle in each embryonic temperature group at 27C and post 30 days acclimation 16C.     Protocols: Zebrafish were raised at temperatures of either 27C or 32C as embryos Adult zebrafish from each embryonic temperature group were acclimated to either 27C or 16C. Epaxial white muscle was then dissected in phosphate buffered saline under a stereomicroscope and then frozen at 80C until RNA extraction. WH1 F M pooled fish SAMEA1487369 Genepool AdultAcclimationTemperature:27 degree C|ENA FIRST PUBLIC:2012 08 21T17:00:45Z|ENA LAST UPDATE:2018 03 08T15:49:00Z|External Id:SAMEA1487369|INSDC center name:Genepool|INSDC first public:2012 08 21T17:00:45Z|INSDC last update:2018 03 08T15:49:00Z|INSDC status:public|Submitter Id:E MTAB 1155:WH1 F M pooled fish|broker name:ArrayExpress|common name:zebrafish|embryonic temperature:32 degree C|sample name:E MTAB 1155:WH1 F M pooled fish|scientific name:Danio rerio|sex:mixed sex                 The effects of temperature on gene expression in zebrafish E MTAB 1155:WH1 seq WH1 pooled extract The effects of temperature on gene expression in zebrafish Trizol based extraction of total RNA from the epaxial white muscle following the manufacturer's Sigma recommendations. Experimental Factor: EmbryonicTemperature:32 degree C|Experimental Factor: AdultAcclimationTemperature:27 degree C RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP001552 Illumina HiSeq 2000 paired end sequencing; The effects of temperature on gene expression in zebrafish ENA FIRST PUBLIC:2012 08 21|ENA LAST UPDATE:2018 11 16 WH1_1.fq.gz WH1_2.fq.gz fastq fastq 3005524064.0 14878832.0 E MTAB 1155:WH1 0:101 1:101 A:780146739;C:722416478;G:730307409;T:771476282;N:1177156 101 101     780146739 722416478 730307409 771476282 1177156 ERX122954 ERS151243 ERA142144 Genepool|Department of Biology, McMaster University Genepool|Department of Biology, McMaster University 2 0.94764 0.92072 0.03746 0.03773 0.83416 0.84831 0.42239 0.51505 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2012-08-21 Adult Adult Whole Organism All anatomical structures
9711 9711 ERR3366000 ERX3390288 ERS3506636 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 3 SAMEA5702979 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702979|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 3|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 3 p WT 5dpf whole 3 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf-whole-3_1.fastq.gz WT-5dpf-whole-3_2.fastq.gz fastq fastq 7638506536.0 25293068.0 E MTAB 8029:WT 5dpf whole 3 0:151 1:151 A:2033085216;C:1787203019;G:1834311569;T:1982924179;N:982553 151 151     2033085216 1787203019 1834311569 1982924179 982553 ERX3390288 ERS3506636 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92943 0.93349 0.06443 0.06476 0.67008 0.68489 0.45244 0.47512 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9712 9712 ERR3365999 ERX3390287 ERS3506635 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 2 SAMEA5702978 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702978|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 2|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 2 p WT 5dpf whole 2 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf--whole-2_1.fastq.gz WT-5dpf--whole-2_2.fastq.gz fastq fastq 8029356446.0 26587273.0 E MTAB 8029:WT 5dpf whole 2 0:151 1:151 A:2111720421;C:1902949602;G:1956400199;T:2057162414;N:1123810 151 151     2111720421 1902949602 1956400199 2057162414 1123810 ERX3390287 ERS3506635 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93664 0.9394 0.06211 0.06234 0.67036 0.68416 0.44709 0.4713 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9713 9713 ERR3365998 ERX3390286 ERS3506634 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. WT 5dpf whole 1 SAMEA5702977 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702977|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:WT 5dpf whole 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wild type genotype|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:WT 5dpf whole 1|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:WT 5dpf whole 1 p WT 5dpf whole 1 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten WT-5dpf-whole-1_1.fastq.gz WT-5dpf-whole-1_2.fastq.gz fastq fastq 7581314682.0 25103691.0 E MTAB 8029:WT 5dpf whole 1 0:151 1:151 A:2028089715;C:1768357820;G:1809746152;T:1974047455;N:1073540 151 151     2028089715 1768357820 1809746152 1974047455 1073540 ERX3390286 ERS3506634 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92712 0.93122 0.06876 0.06853 0.66464 0.67537 0.46592 0.47176 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9714 9714 ERR3365997 ERX3390285 ERS3506633 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c386C T het 5dpf whl2 SAMEA5702976 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702976|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl2|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c386C T het 5dpf whl2 p c386C T het 5dpf whl2 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-2_1.fastq.gz c386C-T-het-5dpf-whl-2_2.fastq.gz fastq fastq 7431512716.0 24607658.0 E MTAB 8029:c386C T het 5dpf whl 2 0:151 1:151 A:1981584337;C:1740735155;G:1776201259;T:1931922393;N:1069572 151 151     1981584337 1740735155 1776201259 1931922393 1069572 ERX3390285 ERS3506633 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.92957 0.933 0.0653 0.06445 0.66967 0.6788 0.46228 0.46392 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9715 9715 ERR3365996 ERX3390284 ERS3506632 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c386C T het 5dpf whl1 SAMEA5702975 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702975|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c386C T het 5dpf whl1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c386C T het 5dpf whl1|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c386C T het 5dpf whl1 p c386C T het 5dpf whl1 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-1_1.fastq.gz c386C-T-het-5dpf-whl-1_2.fastq.gz fastq fastq 7350140024.0 24338212.0 E MTAB 8029:c386C T het 5dpf whl 1 0:151 1:151 A:1930881649;C:1748604586;G:1790297791;T:1879354724;N:1001274 151 151     1930881649 1748604586 1790297791 1879354724 1001274 ERX3390284 ERS3506632 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93663 0.9384 0.05835 0.05828 0.66557 0.67588 0.467 0.46407 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9716 9716 ERR3365995 ERX3390283 ERS3506631 ERP115705 PRJEB32960 RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E-MTAB-8029 Transcriptome Analysis RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos. ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 10   Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. c.386C T het 5dpf whl3 SAMEA5702974 Medical College of Wisconsin ENA FIRST PUBLIC:2019 07 19T04:04:05Z|ENA LAST UPDATE:2019 06 10T11:46:52Z|External Id:SAMEA5702974|INSDC center name:Medical College of Wisconsin|INSDC first public:2019 07 19T04:04:05Z|INSDC last update:2019 06 10T11:46:52Z|INSDC status:public|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval day 5|genotype:wdr37 mutant c.386C>T p.Ser129Phe|individual:mixed pool of 5 embryos|organism part:whole organism|sample name:E MTAB 8029:c.386C T het 5dpf whl3|scientific name:Danio rerio                 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type E MTAB 8029:c.386C T het 5dpf whl3 p c.386C T het 5dpf whl3 p RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F. Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq X Ten   ERP115705 HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type ENA FIRST PUBLIC:2019 07 19|ENA LAST UPDATE:2019 06 12|instrument model:HiSeq X Ten c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz fastq fastq 6059681642.0 20065171.0 E MTAB 8029:c386C T het 5dpf whl 3 0:151 1:151 A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092 151 151     1604034432 1423963595 1467519505 1563303018 861092 ERX3390283 ERS3506631 ERA1993466 European Nucleotide Archive European Nucleotide Archive 2 0.93301 0.9374 0.0658 0.06581 0.66681 0.68503 0.46139 0.47743 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Unknown 2019-06-10 Larval Larval Whole Organism All anatomical structures
9825 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 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 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 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 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 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 10060 ERR4795364 ERX4665135 ERS5281176 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 4 E MTAB 9727:Sample 4   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 4 s Sample 4 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN4_AH2TW3BGX5_S1_R1_cat.fastq.gz fastq 5410723202.0 71707309.0 E MTAB 9727:Sample 4 0:75.46 1:0 A:1330416803;C:531269504;G:734031980;T:2814959249;N:45666 75 0     1330416803 531269504 734031980 2814959249 45666 ERX4665135 ERS5281176 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.33614   0.21532   0.99019   0.41002   76   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10061 10061 ERR4795365 ERX4665135 ERS5281176 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 4 E MTAB 9727:Sample 4   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 4 s Sample 4 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 4 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN4_AH2TW3BGX5_S1_R2_cat.fastq.gz fastq 5414184547.0 71707309.0 E MTAB 9727:Sample 4 1 0:0 1:75.50 A:1582938104;C:1052565419;G:1177180395;T:1600161662;N:1338967 0 75     1582938104 1052565419 1177180395 1600161662 1338967 ERX4665135 ERS5281176 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.84976   0.28521   0.85038   0.5124   75   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10062 10062 ERR4795362 ERX4665134 ERS5281175 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 3 E MTAB 9727:Sample 3   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 3 s Sample 3 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 3 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN3_AHY3WGBGX3_S7_R1_cat.fastq.gz fastq 4823193891.0 63965519.0 E MTAB 9727:Sample 3 0:75.40 1:0 A:1323978162;C:446831209;G:581746343;T:2470114091;N:524086 75 0     1323978162 446831209 581746343 2470114091 524086 ERX4665134 ERS5281175 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.36549   0.19722   0.95552   0.4702   76   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10063 10063 ERR4795363 ERX4665134 ERS5281175 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 3 E MTAB 9727:Sample 3   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 3 s Sample 3 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 3 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN3_AHY3WGBGX3_S7_R2_cat.fastq.gz fastq 4828889391.0 63965519.0 E MTAB 9727:Sample 3 1 0:0 1:75.49 A:1434099697;C:964508763;G:893584575;T:1534727600;N:1968756 0 75     1434099697 964508763 893584575 1534727600 1968756 ERX4665134 ERS5281175 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.85811   0.26231   0.82731   0.48618   76   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10064 10064 ERR4795360 ERX4665133 ERS5281174 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 2 E MTAB 9727:Sample 2   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 2 s Sample 2 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 2 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN2_AHY3WGBGX3_S6_R1_cat.fastq.gz fastq 5598371393.0 74235388.0 E MTAB 9727:Sample 2 0:75.41 1:0 A:1526486973;C:558020193;G:717587491;T:2795646081;N:630655 75 0     1526486973 558020193 717587491 2795646081 630655 ERX4665133 ERS5281174 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.28059   0.19252   0.96404   0.4874   75   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10065 10065 ERR4795361 ERX4665133 ERS5281174 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 2 E MTAB 9727:Sample 2   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 2 s Sample 2 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 2 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN2_AHY3WGBGX3_S6_R2_cat.fastq.gz fastq 5600151371.0 74235388.0 E MTAB 9727:Sample 2 1 0:0 1:75.44 A:1850568176;C:1035622971;G:1071138281;T:1640475883;N:2346060 0 75     1850568176 1035622971 1071138281 1640475883 2346060 ERX4665133 ERS5281174 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.7679   0.30371   0.82651   0.43401   75   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10066 10066 ERR4795358 ERX4665132 ERS5281173 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 1 E MTAB 9727:Sample 1   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 1 s Sample 1 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN1_AHY3WGBGX3_S5_R1_cat.fastq.gz fastq 4996502316.0 66258508.0 E MTAB 9727:Sample 1 0:75.41 1:0 A:1330744174;C:451622042;G:591151500;T:2622422664;N:561936 75 0     1330744174 451622042 591151500 2622422664 561936 ERX4665132 ERS5281173 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.29754   0.17671   0.9669   0.45463   75   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10067 10067 ERR4795359 ERX4665132 ERS5281173 ERP124847 PRJEB41113 Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E-MTAB-9727 Transcriptome Analysis The mesothelium forms epithelial membranes that line the bodies cavities and surround the internal organs. Mesothelia widely contribute to organ homeostasis and regeneration and their dysregulation can result in congenital anomalies of the viscera ventral wall defects and mesothelioma tumors. Nonetheless the embryonic ontogeny and developmental regulation of mesothelium formation has remained uncharted. Here we combine genetic lineage tracing in toto live imaging and single cell transcriptomics in zebrafish to track mesothelial progenitor origins from the lateral plate mesoderm LPM. Our single cell analysis uncovers a post gastrulation gene expression signature centered on hand2 that delineates distinct progenitor populations within the forming LPM. Combining gene expression analysis and imaging of transgenic reporter zebrafish embryos we chart the origin of mesothelial progenitors to the lateral most hand2 expressing LPM and confirm evolutionary conservation in mouse. Our time lapse imaging of transgenic hand2 reporter embryos captures zebrafish mesothelium formation documenting the coordinated cell movements that form pericardium and visceral and parietal peritoneum. We establish that the primordial germ cells migrate associated with the forming mesothelium as ventral migration boundary. Functionally hand2 mutants fail to close the ventral mesothelium due to perturbed migration of mesothelium progenitors. Analyzing mouse and human mesothelioma tumors hypothesized to emerge from transformed mesothelium we find de novo expression of LPM associated transcription factors and in particular of Hand2 indicating the re initiation of a developmental transcriptional program in mesothelioma. Taken together our work outlines a genetic and developmental signature of mesothelial origins centered around Hand2 contributing to our understanding of mesothelial pathologies and mesothelioma. ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14   Protocols: Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse trans… Sample 1 E MTAB 9727:Sample 1   isolate:not applicable|organism:Danio rerio|sex:mixed|age:10|developmental stage:tailbud stage|organism part:lateral plate mesoderm plate|genotype:drl:mCherry|ENA FIRST PUBLIC:2021 04 01|ENA LAST UPDATE:2021 09 01                 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma E MTAB 9727:Sample 1 s Sample 1 s Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma Wildtype stain and drl:mCherry positive zebrafish embryos were grown until tailbud stage and chorions were removed by incubating in 1 mg/mL Pronase Roche followed by washing in E3 medium. Around 300 embryos were used to generate the sample. The E3 medium was replaced by 1X PBS and the embryos were stored on ice until further processing. The embryos were dissociated using 2 mg/mL collagenase IV Worthington in DMEM high glucose 4.5g/l and NaHCO3 without xxx glutamine and sodium pyruvate Sigma Aldrich and incubated for 5 min in a water bath at 37oC. The embryonic tissues were triturated into a single cell suspension by pipetting carefully up and down. When the embryos were not yet dissociated sufficiently they were incubated for another 5 min. Cells were filtered through a 35 μm cell strainer Falcon round bottom tubes with cell strainer cap and centrifuged at 6000 rpm for 30 sec. Cell pellets were resuspended in 1X HBSS Gibco containing 2% FBS and subjected to an additional round of centrifugation and resuspension. post washing the cells were resuspended in 1X PBS. drl:mCherry positive cells were sorted using a FACS Aria III cell sorter BD Bioscience. Cells were gated based on size and forward scattering to exclude debris and doublets. The gating for the negative population was determined based on wildtype tailbud staged embryos. See also Figure S2 for gate setting. The SORTseq single cell RNA sequencing protocol was carried out as described previously Muraro et al. 2016. Live mCherry positive single cells were sorted in four 384 well plates BioRad containing 5 μl of CEL Seq2 primer solution in mineral oil 24 bp polyT stretch a 4 bp random molecular barcode UMI a cell specific barcode the 5′Illumina TruSeq small RNA kit adaptor and a T7 promoter provided by Single Cell Discoveries. post sorting the plates were immediately placed on ice and stored at −80°C. In brief ERCC Spike in RNA 0.02 μL of 1:50000 dilution was added to each well before cell lysis with heat shocking. Reverse transcription an… Experimental Factor: replicate:lateral plate mesoderm plate 1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM SINGLE ILLUMINA NextSeq 500   ERP124847 NextSeq 500 sequencing; Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma ENA FIRST PUBLIC:2022 01 14|ENA LAST UPDATE:2022 01 14 SN1_AHY3WGBGX3_S5_R2_cat.fastq.gz fastq 4999908389.0 66258508.0 E MTAB 9727:Sample 1 1 0:0 1:75.46 A:1591945117;C:933968124;G:986108614;T:1485824022;N:2062512 0 75     1591945117 933968124 986108614 1485824022 2062512 ERX4665132 ERS5281173 ERA3048543 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 1 0.81333   0.2466   0.83027   0.51572   75   B   usable mapping rate illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Switzerland 2021-04-01 Gastrula Embryo Embryo Imprecise All anatomical structures
10374 10374 ERR8058375 ERX7625096 ERS10119356 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 3 SAMEA12512752 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512752|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 3 p Morphine 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4M_lib138515_4790_6_1.fastq.gz NG-10331_4M_lib138515_4790_6_2.fastq.gz fastq fastq 11175776640.0 44348320.0 E MTAB 11346:NG 10331 4M lib138515 4790 6 0:126 1:126 A:3058552548;C:2537121022;G:2531362154;T:3047376587;N:1364329 126 126     3058552548 2537121022 2531362154 3047376587 1364329 ERX7625096 ERS10119356 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93345 0.93836 0.09826 0.09482 0.69497 0.69968 0.46885 0.46966 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10375 10375 ERR8058374 ERX7625095 ERS10119355 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 2 SAMEA12512751 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512751|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 2 p Morphine 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3M_lib138512_4790_5_1.fastq.gz NG-10331_3M_lib138512_4790_5_2.fastq.gz fastq fastq 10428424776.0 41382638.0 E MTAB 11346:NG 10331 3M lib138512 4790 5 0:126 1:126 A:2840226558;C:2379827926;G:2389813154;T:2817428937;N:1128201 126 126     2840226558 2379827926 2389813154 2817428937 1128201 ERX7625095 ERS10119355 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94204 0.9476 0.09827 0.09565 0.7008 0.70483 0.47435 0.47651 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10376 10376 ERR8058373 ERX7625094 ERS10119354 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Morphine 1 SAMEA12512750 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512750|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Morphine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Morphine 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Morphine 1 p Morphine 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:morphine|Experimental Factor: dose:10 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2M_lib138509_4790_5_1.fastq.gz NG-10331_2M_lib138509_4790_5_2.fastq.gz fastq fastq 13158093312.0 52214656.0 E MTAB 11346:NG 10331 2M lib138509 4790 5 0:126 1:126 A:3613282182;C:2969954628;G:2964948806;T:3608471124;N:1436572 126 126     3613282182 2969954628 2964948806 3608471124 1436572 ERX7625094 ERS10119354 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93755 0.93735 0.11204 0.10849 0.67838 0.68335 0.45142 0.46509 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10377 10377 ERR8058372 ERX7625093 ERS10119353 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 3 SAMEA12512749 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512749|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 3 p Control 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4C_lib138514_4790_6_1.fastq.gz NG-10331_4C_lib138514_4790_6_2.fastq.gz fastq fastq 14106514968.0 55978234.0 E MTAB 11346:NG 10331 4C lib138514 4790 6 0:126 1:126 A:3862641975;C:3195634147;G:3187866318;T:3858673135;N:1699393 126 126     3862641975 3195634147 3187866318 3858673135 1699393 ERX7625093 ERS10119353 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93657 0.93813 0.09783 0.09438 0.68925 0.69605 0.4741 0.47037 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10378 10378 ERR8058371 ERX7625092 ERS10119352 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 2 SAMEA12512748 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512748|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 2 p Control 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3C_lib138511_4790_5_1.fastq.gz NG-10331_3C_lib138511_4790_5_2.fastq.gz fastq fastq 8889952680.0 35277590.0 E MTAB 11346:NG 10331 3C lib138511 4790 5 0:126 1:126 A:2424658667;C:2024699093;G:2023098669;T:2416527349;N:968902 126 126     2424658667 2024699093 2023098669 2416527349 968902 ERX7625092 ERS10119352 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94168 0.94149 0.09632 0.09404 0.68996 0.69672 0.46007 0.47123 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10379 10379 ERR8058370 ERX7625091 ERS10119351 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Control 1 SAMEA12512747 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512747|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Control 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Control 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Control 1 p Control 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:n1 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2C_lib138508_4790_5_1.fastq.gz NG-10331_2C_lib138508_4790_5_2.fastq.gz fastq fastq 12714421356.0 50454053.0 E MTAB 11346:NG 10331 2C lib138508 4790 5 0:126 1:126 A:3470625985;C:2894721473;G:2886656166;T:3461036460;N:1381272 126 126     3470625985 2894721473 2886656166 3461036460 1381272 ERX7625091 ERS10119351 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93951 0.93975 0.10489 0.10173 0.68134 0.68702 0.45337 0.44545 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10380 10380 ERR8058369 ERX7625090 ERS10119350 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 3 SAMEA12512746 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512746|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 3|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 3 p Cocaine 3 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_4CC_lib138516_4790_6_1.fastq.gz NG-10331_4CC_lib138516_4790_6_2.fastq.gz fastq fastq 9574359984.0 37993492.0 E MTAB 11346:NG 10331 4CC lib138516 4790 6 0:126 1:126 A:2623103101;C:2170327733;G:2166494677;T:2613276955;N:1157518 126 126     2623103101 2170327733 2166494677 2613276955 1157518 ERX7625090 ERS10119350 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.9366 0.93856 0.10196 0.09901 0.69018 0.69611 0.46501 0.46917 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10381 10381 ERR8058368 ERX7625089 ERS10119349 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 2 SAMEA12512745 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512745|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 2|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 2 p Cocaine 2 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_3CC_lib138513_4828_1_1.fastq.gz NG-10331_3CC_lib138513_4828_1_2.fastq.gz fastq fastq 6977861604.0 27689927.0 E MTAB 11346:NG 10331 3CC lib138513 4828 1 0:126 1:126 A:1938593544;C:1560242508;G:1564690065;T:1913028128;N:1307359 126 126     1938593544 1560242508 1564690065 1913028128 1307359 ERX7625089 ERS10119349 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.94226 0.9472 0.10354 0.10202 0.69911 0.69891 0.4749 0.47595 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
10382 10382 ERR8058367 ERX7625088 ERS10119348 ERP134902 PRJEB50332 RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E-MTAB-11346 Transcriptome Analysis To determine the transcriptomic changes elicted by drugs of abuse zebrafish embryos were exposed to 10uM morphine from xxx hpf ttwo xxx hpf. Embryos were euthanized and deep frozen with N2l. RNA was extracted and an RNA seq assay was performed with Illumina Platform ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03   Protocols: At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Cocaine 1 SAMEA12512744 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain. ENA FIRST PUBLIC:2022 12 31|ENA LAST UPDATE:2022 12 31|External Id:SAMEA12512744|INSDC center alias:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC center name:Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon INCyL. University of Salamanca Spain.|INSDC first public:2022 12 31T00:57:45Z|INSDC last update:2022 12 31T00:57:45Z|INSDC status:public|Submitter Id:E MTAB 11346:Cocaine 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|developmental stage:72|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11346:Cocaine 1|strain:AB                 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine E MTAB 11346:Cocaine 1 p Cocaine 1 p RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine At 72 hpf embryos were sacrificed by cold exposure incubating the multiwell plates on crushed ice. Embryos were transferred to eppendorfs medium was removed and they were frozen in N2l. Tissue was stored at 80ºC until use. RNA was obtained using PureLinkTM RNA Mini Kit Ambion Fisher Scientific following the manufacturer´s instructions. In column DNase I digestion Invitrogen Fisher Scientific was performed to remove the traces of gDNA. RNA concentration was initially determined with a NanoDrop 2000C spectrophotometer Thermo Scientific the purity of the sample was established according to the ratio of absorbances measured at 260/280 nm and RNA integrity was check with a Bioanalyzer RNA Agilent. Ribosomal RNA was depleted using RiboMinus™ RNA was fragmented reverse transcrided using random hexamers three prime and five prime adapters were attached and library was amplified by PCR Experimental Factor: compound:cocaine|Experimental Factor: dose:15 RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP134902 Illumina HiSeq 4000 paired end sequencing; RNA seq pf zebrafish embryos treated with drugs of abuse morphine and cocaine ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03 NG-10331_2CC_lib138510_4790_5_1.fastq.gz NG-10331_2CC_lib138510_4790_5_2.fastq.gz fastq fastq 13608728532.0 54002891.0 E MTAB 11346:NG 10331 2CC lib138510 4790 5 0:126 1:126 A:3713185950;C:3097562409;G:3088976816;T:3707538756;N:1464601 126 126     3713185950 3097562409 3088976816 3707538756 1464601 ERX7625088 ERS10119348 ERA8439547 Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive Dept. Biochemistry and Molecular Biology. Faculty of Medicine. Instituto de Neurociencias de Castilla y Leon (INCyL). University of Salamanca, Spain.|European Nucleotide Archive 2 0.93921 0.94011 0.104 0.10075 0.68043 0.68523 0.44482 0.4591 126 126 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Spain 2022-12-31 Larval Larval Whole Organism All anatomical structures
11238 11238 ERR10782555 ERX10233132 ERS14439197 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 6 E MTAB 12503:Sample 6   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 6 p Sample 6 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz fastq fastq 14809693138.0 49038719.0 E MTAB 12503:20170530.A 6 R 0:151 1:151 A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269 151 151     4069749497 3367864217 3430269434 3928390721 13419269 ERX10233132 ERS14439197 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.83945 0.69977 0.27269 0.22488 0.74523 0.77654 0.4899 0.4358 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11239 11239 ERR10782554 ERX10233131 ERS14439196 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 5 E MTAB 12503:Sample 5   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 5 p Sample 5 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz fastq fastq 14954968728.0 49519764.0 E MTAB 12503:20170530.A 5 R 0:151 1:151 A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280 151 151     4063340262 3440933120 3455723079 3981396987 13575280 ERX10233131 ERS14439196 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.85891 0.86859 0.28842 0.28866 0.7349 0.75051 0.45532 0.49145 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11240 11240 ERR10782553 ERX10233130 ERS14439195 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 2 E MTAB 12503:Sample 2   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 2 p Sample 2 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz fastq fastq 16267571562.0 53866131.0 E MTAB 12503:20170530.A 2 R 0:151 1:151 A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668 151 151     4395815325 3765428574 3780844712 4310729283 14753668 ERX10233130 ERS14439195 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.86977 0.8727 0.28497 0.28427 0.70763 0.72301 0.47478 0.47986 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11241 11241 ERR10782552 ERX10233129 ERS14439194 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 1 E MTAB 12503:Sample 1   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 1 p Sample 1 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz fastq fastq 15446599662.0 51147681.0 E MTAB 12503:20170530.A 1 R 0:151 1:151 A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332 151 151     4289931639 3451135010 3474244788 4217248893 14039332 ERX10233129 ERS14439194 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.90114 0.90507 0.32128 0.32127 0.70232 0.71956 0.47336 0.47528 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11242 11242 ERR10782551 ERX10233128 ERS14439193 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 7 E MTAB 12503:Sample 7   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 7 p Sample 7 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz fastq fastq 12726557236.0 42140918.0 E MTAB 12503:20170530.A 7 R 0:151 1:151 A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382 151 151     3510176970 2879679978 2932244172 3392911734 11544382 ERX10233128 ERS14439193 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88531 0.88678 0.33279 0.3329 0.73545 0.74992 0.52548 0.52864 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11243 11243 ERR10782550 ERX10233127 ERS14439192 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 4 E MTAB 12503:Sample 4   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 4 p Sample 4 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz fastq fastq 15697575554.0 51978727.0 E MTAB 12503:20170530.A 4 R 0:151 1:151 A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133 151 151     4256444510 3622485921 3650190489 4154211501 14243133 ERX10233127 ERS14439192 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.87714 0.88071 0.29319 0.29235 0.69844 0.7164 0.47594 0.47385 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11244 11244 ERR10782549 ERX10233126 ERS14439191 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 3 E MTAB 12503:Sample 3   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 3 p Sample 3 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz fastq fastq 13839085674.0 45824787.0 E MTAB 12503:20170530.A 3 R 0:151 1:151 A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362 151 151     3812423011 3120168590 3163957945 3729983766 12552362 ERX10233126 ERS14439191 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88987 0.74432 0.33651 0.27875 0.69229 0.72934 0.46981 0.46116 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11747 11747 ERR11608177 ERX11010308 ERS15939662 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU2 SAMEA113945412 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945412|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU2|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU2|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU2 p MU2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU2_R1.fastq.gz MU2_R2.fastq.gz fastq fastq 8373912900.0 27913043.0 E MTAB 13116:MU2 R 0:150 1:150 A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489 150 150     2149105370 2028251580 2055193482 2141168979 193489 ERX11010308 ERS15939662 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11748 11748 ERR11608179 ERX11010310 ERS15939664 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT1 SAMEA113945414 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945414|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:WT1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:WT1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT1 p WT1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT1_R1.fastq.gz WT1_R2.fastq.gz fastq fastq 6729388500.0 22431295.0 E MTAB 13116:WT1 R 0:150 1:150 A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873 150 150     1730015872 1621295817 1657133586 1720858352 84873 ERX11010310 ERS15939664 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11749 11749 ERR11608176 ERX11010307 ERS15939661 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU1 SAMEA113945411 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945411|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU1 p MU1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU1_R1.fastq.gz MU1_R2.fastq.gz fastq fastq 7310352000.0 24367840.0 E MTAB 13116:MU1 R 0:150 1:150 A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432 150 150     1888660247 1748082353 1788562372 1884958596 88432 ERX11010307 ERS15939661 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11750 11750 ERR11608178 ERX11010309 ERS15939663 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU3 SAMEA113945413 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945413|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU3|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU3|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU3 p MU3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU3_R1.fastq.gz MU3_R2.fastq.gz fastq fastq 8826207900.0 29420693.0 E MTAB 13116:MU3 R 0:150 1:150 A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162 150 150     2298326835 2100185951 2130807919 2296678033 209162 ERX11010309 ERS15939663 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11751 11751 ERR11608180 ERX11010311 ERS15939665 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT2 E MTAB 13116:WT2   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT2 p WT2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT2_R1.fastq.gz WT2_R2.fastq.gz fastq fastq 8368621500.0 27895405.0 E MTAB 13116:WT2 R 0:150 1:150 A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219 150 150     2126734187 2050458346 2078646608 2112586140 196219 ERX11010311 ERS15939665 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11752 11752 ERR11608181 ERX11010312 ERS15939666 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT3 E MTAB 13116:WT3   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT3 p WT3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT3_R1.fastq.gz WT3_R2.fastq.gz fastq fastq 8718445500.0 29061485.0 E MTAB 13116:WT3 R 0:150 1:150 A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540 150 150     2244668655 2103611849 2135345835 2234609621 209540 ERX11010312 ERS15939666 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
32018 32018 SRR28960817 SRX24490444 SRS21239720 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty RGNNV 2   strain:wild type|isolate:10|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty RGNNV 2 Empty RGNNV 2 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-V2_2.fastq.gz C-V2_1.fastq.gz fastq fastq 4988932790.0 16519645.0 C V2 1.fastq.gz 0:151 1:151 A:1355149914;C:1135513565;G:1149109922;T:1349135360;N:24029 151 151     1355149914 1135513565 1149109922 1349135360 24029 SRX24490444 SRS21239720 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94379 0.94549 0.11621 0.11505 0.65423 0.65577 0.48135 0.48232 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32019 32019 SRR28960818 SRX24490443 SRS21239719 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty RGNNV 1   strain:wild type|isolate:9|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty RGNNV 1 Empty RGNNV 1 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-V1_2.fastq.gz C-V1_1.fastq.gz fastq fastq 5032900970.0 16665235.0 C V1 1.fastq.gz 0:151 1:151 A:1378766254;C:1133849186;G:1146563693;T:1373698300;N:23537 151 151     1378766254 1133849186 1146563693 1373698300 23537 SRX24490443 SRS21239719 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.9444 0.94533 0.11258 0.11038 0.65194 0.65259 0.48812 0.48428 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32020 32020 SRR28960819 SRX24490442 SRS21239718 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp C4   strain:wild type|isolate:8|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp C4 igldcp C4 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-C4_2.fastq.gz G17-C4_1.fastq.gz fastq fastq 5008644028.0 16584914.0 G17 C4 1.fastq.gz 0:151 1:151 A:1365541116;C:1135139643;G:1150040618;T:1357899842;N:22809 151 151     1365541116 1135139643 1150040618 1357899842 22809 SRX24490442 SRS21239718 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94527 0.94533 0.10689 0.10479 0.65535 0.65681 0.47637 0.48487 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32021 32021 SRR28960820 SRX24490441 SRS21239717 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp C3   strain:wild type|isolate:7|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp C3 igldcp C3 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-C3_2.fastq.gz G17-C3_1.fastq.gz fastq fastq 4980119222.0 16490461.0 G17 C3 1.fastq.gz 0:151 1:151 A:1360303556;C:1126738486;G:1145297479;T:1347756591;N:23110 151 151     1360303556 1126738486 1145297479 1347756591 23110 SRX24490441 SRS21239717 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.9466 0.94717 0.11289 0.11094 0.66257 0.66464 0.47181 0.47916 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32022 32022 SRR28960821 SRX24490440 SRS21239716 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp C2   strain:wild type|isolate:6|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp C2 igldcp C2 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-C2_2.fastq.gz G17-C2_1.fastq.gz fastq fastq 5007933422.0 16582561.0 G17 C2 1.fastq.gz 0:151 1:151 A:1372213671;C:1129918132;G:1143655284;T:1362122899;N:23436 151 151     1372213671 1129918132 1143655284 1362122899 23436 SRX24490440 SRS21239716 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94572 0.94517 0.11003 0.10818 0.65658 0.65805 0.4773 0.48344 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32023 32023 SRR28960822 SRX24490439 SRS21239715 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp C1   strain:wild type|isolate:5|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp C1 igldcp C1 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-C1_1.fastq.gz G17-C1_2.fastq.gz fastq fastq 5024913070.0 16638785.0 G17 C1 1.fastq.gz 0:151 1:151 A:1380366672;C:1129585807;G:1150817244;T:1364119307;N:24040 151 151     1380366672 1129585807 1150817244 1364119307 24040 SRX24490439 SRS21239715 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94287 0.94431 0.11558 0.11383 0.65277 0.65382 0.4826 0.48102 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32024 32024 SRR28960823 SRX24490438 SRS21239714 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty C4   strain:wild type|isolate:4|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty C4 Empty C4 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-C4_2.fastq.gz C-C4_1.fastq.gz fastq fastq 4979945874.0 16489887.0 C C4 1.fastq.gz 0:151 1:151 A:1355600042;C:1132041799;G:1147315384;T:1344965018;N:23631 151 151     1355600042 1132041799 1147315384 1344965018 23631 SRX24490438 SRS21239714 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94757 0.94857 0.10346 0.10203 0.65539 0.65673 0.4708 0.46117 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32025 32025 SRR28960827 SRX24490437 SRS21239713 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty C3   strain:wild type|isolate:3|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty C3 Empty C3 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-C3_2.fastq.gz C-C3_1.fastq.gz fastq fastq 5029174894.0 16652897.0 C C3 1.fastq.gz 0:151 1:151 A:1374911488;C:1136783068;G:1150269816;T:1367186209;N:24313 151 151     1374911488 1136783068 1150269816 1367186209 24313 SRX24490437 SRS21239713 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94336 0.94484 0.11529 0.11371 0.65305 0.65488 0.47386 0.4875 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32026 32026 SRR28960824 SRX24490436 SRS21239712 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp RGNNV 4   strain:wild type|isolate:15|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp RGNNV 4 igldcp RGNNV 4 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-V4_1.fastq.gz G17-V4_2.fastq.gz fastq fastq 5038044634.0 16682267.0 G17 V4 1.fastq.gz 0:151 1:151 A:1373754614;C:1142848550;G:1159235100;T:1362182221;N:24149 151 151     1373754614 1142848550 1159235100 1362182221 24149 SRX24490436 SRS21239712 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94236 0.94358 0.10841 0.10623 0.65429 0.65512 0.47952 0.47896 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32027 32027 SRR28960825 SRX24490435 SRS21239711 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp RGNNV 2   strain:wild type|isolate:14|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp RGNNV 2 igldcp RGNNV 2 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-V2_2.fastq.gz G17-V2_1.fastq.gz fastq fastq 4992836442.0 16532571.0 G17 V2 1.fastq.gz 0:151 1:151 A:1370989397;C:1121917932;G:1135482493;T:1364423268;N:23352 151 151     1370989397 1121917932 1135482493 1364423268 23352 SRX24490435 SRS21239711 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94244 0.94361 0.11703 0.11517 0.65297 0.65305 0.47906 0.47762 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32028 32028 SRR28960826 SRX24490434 SRS21239710 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         igldcp RGNNV 1   strain:wild type|isolate:13|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae igldcp RGNNV 1 igldcp RGNNV 1 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     G17-V1_2.fastq.gz G17-V1_1.fastq.gz fastq fastq 5022577402.0 16631051.0 G17 V1 1.fastq.gz 0:151 1:151 A:1373133624;C:1136711402;G:1147351250;T:1365356916;N:24210 151 151     1373133624 1136711402 1147351250 1365356916 24210 SRX24490434 SRS21239710 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94548 0.9457 0.11091 0.10876 0.6566 0.65794 0.47672 0.47334 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32029 32029 SRR28960828 SRX24490433 SRS21239709 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty RGNNV 4   strain:wild type|isolate:12|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty RGNNV 4 Empty RGNNV 4 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-V4_1.fastq.gz C-V4_2.fastq.gz fastq fastq 4996580940.0 16544970.0 C V4 1.fastq.gz 0:151 1:151 A:1365771383;C:1129645420;G:1139771568;T:1361369690;N:22879 151 151     1365771383 1129645420 1139771568 1361369690 22879 SRX24490433 SRS21239709 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94201 0.94399 0.10865 0.10729 0.65295 0.65397 0.47378 0.48264 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32030 32030 SRR28960829 SRX24490432 SRS21239708 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty RGNNV 3   strain:wild type|isolate:11|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty RGNNV 3 Empty RGNNV 3 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-V3_1.fastq.gz C-V3_2.fastq.gz fastq fastq 4990782540.0 16525770.0 C V3 1.fastq.gz 0:151 1:151 A:1370883963;C:1121960304;G:1139361266;T:1358553278;N:23729 151 151     1370883963 1121960304 1139361266 1358553278 23729 SRX24490432 SRS21239708 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94311 0.94426 0.10644 0.10476 0.65535 0.65756 0.46134 0.44955 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32031 32031 SRR28960830 SRX24490431 SRS21239707 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty C2   strain:wild type|isolate:2|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty C2 Empty C2 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-C2_2.fastq.gz C-C2_1.fastq.gz fastq fastq 4991313154.0 16527527.0 C C2 1.fastq.gz 0:151 1:151 A:1366713096;C:1125818845;G:1141236594;T:1357520576;N:24043 151 151     1366713096 1125818845 1141236594 1357520576 24043 SRX24490431 SRS21239707 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94263 0.94476 0.10847 0.10745 0.65928 0.65904 0.47366 0.47959 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32032 32032 SRR28960831 SRX24490430 SRS21239702 SRP506336 PRJNA1108487 First formal characterization of the fish specific molecule Immunoglobulin like domain containing protein Igldcp in zebrafish Danio rerio: clues about its implication in the immune response PRJNA1108487 Other Numerous evidences demonstrate that the fish exclusive gene immunoglobulin Ig like domain containing protein igldcp is involved in the protection against viruses. Because of this we wanted to study its mode of action in the model species zebrafish Danio rerio. RNA Seq analyses of zebrafish larvae overexpressing or not igldcp and in the presence or absence of an infection with the nodavirus RGNNV were conducted.         Empty C1   strain:wild type|isolate:1|age:4 dpf|dev stage:larvae|collection date:2023|geo loc name:Spain: Vigo|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 Rna Seq of zebrafish larvae Empty C1 Empty C1 RNA from the different pooled samples 3 larvae/sample was isolated using the Maxwell RSC simplyRNA Tissue Kit Promega with an automated Maxwell RSC 48 Instrument in accordance with the instructions provided by the manufacturer. The quantity of RNA was measured on a Qubit 4 fluorometer Thermo Fisher Scientific and RNA integrity was analysed in an Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturer's instructions.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506336     C-C1_1.fastq.gz C-C1_2.fastq.gz fastq fastq 5031068434.0 16659167.0 C C1 1.fastq.gz 0:151 1:151 A:1369231804;C:1143688515;G:1163238884;T:1354885267;N:23964 151 151     1369231804 1143688515 1163238884 1354885267 23964 SRX24490430 SRS21239702 SRA1861741 IIM-CSIC|Immunology and Genomics IIM-CSIC 2 0.94547 0.94589 0.10958 0.10835 0.6564 0.6565 0.48608 0.48591 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Spain 2024-05-08 Larval Larval Whole Organism All anatomical structures
32370 32370 SRR29180530 SRX24700714 SRS21428245 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         DES   isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal                 RNA seq of DES treated DES DES Sequencing the transcriptomes of zebrafish embryos of DES treated     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 4000   SRP509851     DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz fastq fastq 9169560000.0 30565200.0 DES TAAGGC L001 R1 001.fastq.gz 0:150 1:150 A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630 150 150     2545096687 2037322055 2024787099 2562124529 229630 SRX24700714 SRS21428245 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
32371 32371 SRR29180531 SRX24700713 SRS21428246 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.         IOX   isolate:exposure to IOX|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to IOX|BioSampleModel:Model organism or animal                 RNA seq of IOX treated IOX IOX Sequencing the transcriptomes of zebrafish embryos of IOX treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz fastq fastq 9547157100.0 31823857.0 IOX CGTACT L001 R1 001.fastq.gz 0:150 1:150 A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429 150 150     2631030736 2146265744 2124421595 2645201596 237429 SRX24700713 SRS21428246 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
32372 32372 SRR29180532 SRX24700712 SRS21428244 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.         CTR   isolate:control|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal                 RNA seq of CTR treated CTR CTR Sequencing the transcriptomes of zebrafish embryos of control     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz fastq fastq 9602954100.0 32009847.0 CTR AGGCAG L001 R1 001.fastq.gz 0:150 1:150 A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825 150 150     2637866848 2169057233 2152906664 2642882530 240825 SRX24700712 SRS21428244 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
39756 39756 SRR2125736 SRX1117105 SRS1010315 SRP061528 PRJNA290839 Danio rerio Transcriptome or Gene expression PRJNA290839 Transcriptome Analysis RNA Seq of Danio rerio transcriptome         Polr1c2   breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish Polr1c2|treatment:KO|BioSampleModel:Model organism or animal                 RNA Seq of Polr1c2 RNA Seq of Polr1c2 1 Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP061528     Polr1c2_S2_L001_R1_001.fastq.gz Polr1c2_S2_L001_R2_001.fastq.gz bam fastq 1024040592.0 3467167.0 RNA Seq of Polr1c2 0:147.69 1:147.67 A:280222262;C:231619577;G:229733851;T:282415559;N:49343 147 147     280222262 231619577 229733851 282415559 49343 SRX1117105 SRS1010315 SRA279862 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.94843 0.95151 0.09589 0.09554 0.68747 0.68694 0.48798 0.48429 150 151 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk bulk bulk   China 2016-07-24 Larval Larval Whole Organism All anatomical structures
39757 39757 SRR2125735 SRX1117104 SRS1010314 SRP061528 PRJNA290839 Danio rerio Transcriptome or Gene expression PRJNA290839 Transcriptome Analysis RNA Seq of Danio rerio transcriptome         polr1cKO   breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of polr1cKO|treatment:KO|BioSampleModel:Model organism or animal                 RNA Seq of polr1cKO RNA Seq of polr1cKO 1 Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP061528     polr1cKO_S2_L001_R2_001.fastq.gz polr1cKO_S2_L001_R1_001.fastq.gz fastq fastq 2153644339.0 7160972.0 RNA Seq of polr1cKO 0:150.40 1:150.34 A:558724957;C:517375772;G:514543839;T:562990605;N:9166 150 150     558724957 517375772 514543839 562990605 9166 SRX1117104 SRS1010314 SRA279862 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95998 0.9611 0.07455 0.0729 0.65354 0.65496 0.45853 0.46158 151 151 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk bulk bulk   China 2015-07-24 Larval Larval Whole Organism All anatomical structures
39758 39758 SRR2125734 SRX1117103 SRS1010313 SRP061528 PRJNA290839 Danio rerio Transcriptome or Gene expression PRJNA290839 Transcriptome Analysis RNA Seq of Danio rerio transcriptome         AB2   breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of AB2|treatment:WT|BioSampleModel:Model organism or animal                 RNA Seq of AB2 RNA Seq of AB2 1 Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP061528     AB2_S1_L001_R2_001.fastq.gz AB2_S1_L001_R1_001.fastq.gz fastq fastq 829696252.0 2784590.0 RNA Seq of AB2 0:149.00 1:148.96 A:218353676;C:195998962;G:195017076;T:220297820;N:28718 149 148     218353676 195998962 195017076 220297820 28718 SRX1117103 SRS1010313 SRA279862 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96274 0.96494 0.05571 0.05462 0.73588 0.73657 0.48938 0.48219 149 151 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk bulk bulk   China 2015-07-24 Larval Larval Whole Organism All anatomical structures
39759 39759 SRR2125733 SRX1117102 SRS1010312 SRP061528 PRJNA290839 Danio rerio Transcriptome or Gene expression PRJNA290839 Transcriptome Analysis RNA Seq of Danio rerio transcriptome         WT   breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of WT|treatment:WT|BioSampleModel:Model organism or animal                 RNA Seq of WT RNA Seq of WT 1 Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer’s instruction and index codes were ligated as identification to individual samples as previous described. Briefly mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase followed by 3’ end adenylation. post adenylation of 3’ ends of DNA fragments Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP061528     wt_S1_L001_R1_001.fastq.gz wt_S1_L001_R2_001.fastq.gz fastq fastq 1937209279.0 6445507.0 RNA Seq of WT 0:150.30 1:150.25 A:496555264;C:470694471;G:467911055;T:502040892;N:7597 150 150     496555264 470694471 467911055 502040892 7597 SRX1117102 SRS1010312 SRA279862 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95931 0.96087 0.06913 0.06787 0.66101 0.66431 0.45529 0.4629 151 151 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk bulk bulk   China 2016-07-24 Larval Larval Whole Organism All anatomical structures
39911 39911 SRR2255651 SRX1187765 SRS1056695 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           TRAPPC11 Mutant2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant2|BioSampleModel:Model organism or animal                 TRAPPC11 Mutant2 TRAPPC11 Mutant2 TRAPPC11 Mutant2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     fattyliver2_S6_L001_R1_001.fastq.gz fattyliver2_S6_L001_R2_001.fastq.gz fastq fastq 836752562.0 5540752.0 TRAPPC11 Mutant2 0:75.54 1:75.48 A:219401421;C:198252489;G:195663968;T:223211242;N:223442 75 75     219401421 198252489 195663968 223211242 223442 SRX1187765 SRS1056695 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96204 0.96259 0.05777 0.05527 0.74142 0.74089 0.47566 0.47333 75 52 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39912 39912 SRR2255629 SRX1187764 SRS1056694 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           TRAPPC11 Mutant1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant1|BioSampleModel:Model organism or animal                 TRAPPC11 Mutant1 TRAPPC11 Mutant1 TRAPPC11 Mutant1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     fattyliver1_S5_L001_R1_001.fastq.gz fattyliver1_S5_L001_R2_001.fastq.gz fastq fastq 752730180.0 4984563.0 TRAPPC11 Mutant1 0:75.53 1:75.48 A:201453785;C:174638707;G:171041330;T:205386632;N:209726 75 75     201453785 174638707 171041330 205386632 209726 SRX1187764 SRS1056694 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95653 0.95631 0.07274 0.06976 0.70573 0.70664 0.49403 0.49925 74 76 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2015-09-05 Larval Larval Embryo Imprecise All anatomical structures
39913 39913 SRR2255628 SRX1187763 SRS1056693 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           PFOS2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS2|BioSampleModel:Model organism or animal                 PFOS2 PFOS2 PFOS2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     PFOS2_S4_L001_R1_001.fastq.gz PFOS2_S4_L001_R2_001.fastq.gz fastq fastq 660339622.0 4372724.0 PFOS2 0:75.53 1:75.48 A:174477377;C:155458423;G:152138367;T:178072878;N:192577 75 75     174477377 155458423 152138367 178072878 192577 SRX1187763 SRS1056693 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95841 0.95943 0.06213 0.06061 0.71664 0.71717 0.49605 0.5046 76 52 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39914 39914 SRR2255627 SRX1187762 SRS1056692 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           PFOS1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal                 PFOS1 PFOS1 PFOS1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz fastq fastq 791950817.0 5244084.0 PFOS1 0:75.53 1:75.48 A:207476025;C:187690975;G:185784999;T:210781701;N:217117 75 75     207476025 187690975 185784999 210781701 217117 SRX1187762 SRS1056692 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96195 0.96213 0.051 0.04857 0.7386 0.73927 0.49669 0.49151 76 53 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39915 39915 SRR2255626 SRX1187761 SRS1056691 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           DMSO2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO2|BioSampleModel:Model organism or animal                 DMSO2 DMSO2 DMSO2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     DMSO2_S2_L001_R1_001.fastq.gz DMSO2_S2_L001_R2_001.fastq.gz fastq fastq 847975709.0 5615263.0 DMSO2 0:75.53 1:75.48 A:222828293;C:200598370;G:196827420;T:227477582;N:244044 75 75     222828293 200598370 196827420 227477582 244044 SRX1187761 SRS1056691 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95825 0.95852 0.06376 0.06156 0.71224 0.71313 0.49629 0.49076 76 76 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39916 39916 SRR2255625 SRX1187760 SRS1056690 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           DMSO1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO1|BioSampleModel:Model organism or animal                 DMSO1 DMSO1 DMSO1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     DMSO1_S1_L001_R1_001.fastq.gz DMSO1_S1_L001_R2_001.fastq.gz fastq fastq 825003413.0 5463030.0 DMSO1 0:75.53 1:75.48 A:217714985;C:193454273;G:192078021;T:221527657;N:228477 75 75     217714985 193454273 192078021 221527657 228477 SRX1187760 SRS1056690 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96443 0.9657 0.05205 0.04878 0.76581 0.76465 0.49046 0.47298 76 54 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
41782 41782 SRR5162099 SRX2480053 SRS1910957 SRP096313 PRJNA360680 S6K1 project raw sequence reads PRJNA360680 Other           PLC5shCtrl1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shCtrl1|BioSampleModel:Model organism or animal                 PLC5shCtrl1 PLC5shCtrl1 PLC5shCtrl1 Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE COMPLETE_GENOMICS Complete Genomics   SRP096313         1201388650.0 24027773.0 CL100006841 L02 24 1.fq.gz 0:50 A:297299471;C:292335863;G:332701724;T:278571616;N:479976 50       297299471 292335863 332701724 278571616 479976 SRX2480053 SRS1910957 SRA525651 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong|School of Life Sciences 1 0.00295   0.00039   0.99754   0.63223   50   T   under 1.2% mapping rate legacy early unknown random_priming unknown bulk unknown unknown   China 2017-01-10 Larval Larval Embryo Imprecise All anatomical structures
41783 41783 SRR5162098 SRX2480052 SRS1910956 SRP096313 PRJNA360680 S6K1 project raw sequence reads PRJNA360680 Other           Hep3BshS6K1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshS6K1|BioSampleModel:Model organism or animal                 Hep3BshS6K1 Hep3BshS6K1 Hep3BshS6K1 Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE COMPLETE_GENOMICS Complete Genomics   SRP096313         1205347750.0 24106955.0 CL100006841 L02 21 1.fq.gz 0:50 A:312935885;C:282462046;G:322914710;T:286516924;N:518185 50       312935885 282462046 322914710 286516924 518185 SRX2480052 SRS1910956 SRA525651 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong|School of Life Sciences 1 0.00262   0.00033   0.99764   0.69195   50   T   under 1.2% mapping rate legacy early unknown random_priming unknown bulk unknown unknown   China 2017-01-10 Larval Larval Embryo Imprecise All anatomical structures
41784 41784 SRR5162097 SRX2480051 SRS1910955 SRP096313 PRJNA360680 S6K1 project raw sequence reads PRJNA360680 Other           PLC5shS6K1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shS6K1|BioSampleModel:Model organism or animal                 PLC5shS6K1 PLC5shS6K1 PLC5shS6K1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE COMPLETE_GENOMICS Complete Genomics   SRP096313         1205157400.0 24103148.0 CL100006841 L02 25 1.fq.gz 0:50 A:305738728;C:286350102;G:329378158;T:283136091;N:554321 50       305738728 286350102 329378158 283136091 554321 SRX2480051 SRS1910955 SRA525651 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong|School of Life Sciences 1 0.00275   0.00036   0.99801   0.66666   50   T   under 1.2% mapping rate legacy early unknown random_priming unknown bulk unknown unknown   China 2017-01-10 Larval Larval Embryo Imprecise All anatomical structures
41785 41785 SRR5162096 SRX2480050 SRS1910954 SRP096313 PRJNA360680 S6K1 project raw sequence reads PRJNA360680 Other           HepG2shS6K1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shS6K1|BioSampleModel:Model organism or animal                 HepG2shS6K1 HepG2shS6K1 HepG2shS6K1 Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE COMPLETE_GENOMICS Complete Genomics   SRP096313         1203548150.0 24070963.0 CL100006841 L02 23 1.fq.gz 0:50 A:307598832;C:285812241;G:331356323;T:278082314;N:698440 50       307598832 285812241 331356323 278082314 698440 SRX2480050 SRS1910954 SRA525651 The Chinese University of Hong Kong|School of Life Sciences The Chinese University of Hong Kong|School of Life Sciences 1 0.00192   0.00012   0.99784   0.60818   50   T   under 1.2% mapping rate legacy early unknown random_priming unknown bulk unknown unknown   China 2017-01-10 Larval Larval Embryo Imprecise All anatomical structures

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