rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 8088,ERR034127,ERX012653,ERS032268,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 50% epiboly stage,zebrafish embryo 50 epiboly,SAMEA791629,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 50epiboly,JKE Drerio rna seq,Transcriptome profiling of 50% epiboly stages of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz,SOLiD_native SOLiD_native,3929903550.0,78598071.0,KI BN JKE DRERIO RNASEQ 2011 50epiboly,0:50,,50,,,,,,,,,ERX012653,ERS032268,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.60757,,0.09893,,0.94899,,0.77821,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 8089,ERR034126,ERX012652,ERS032267,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 512 cell stage,zebrafish embryo 512 cell,SAMEA791632,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 512cell,JKE Drerio rna seq,Transcriptome profiling of 512 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz,SOLiD_native SOLiD_native,3918756250.0,78375125.0,KI BN JKE DRERIO RNASEQ 2011 512cell,0:50,,50,,,,,,,,,ERX012652,ERS032267,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.63824,,0.09111,,0.91969,,0.73496,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Blastula,Embryo,Embryo Imprecise,All anatomical structures 8090,ERR034125,ERX012651,ERS032266,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 16 cell stage,zebrafish embryo 16 cell,SAMEA791631,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 16cell,JKE Drerio rna seq,Transcriptome profiling of 16 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,ERP000635,AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development,ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16,KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz,SOLiD_native SOLiD_native,4256756500.0,85135130.0,KI BN JKE DRERIO RNASEQ 2011 16cell,0:50,,50,,,,,,,,,ERX012651,ERS032266,ERA029959,KI-BN|Department of Biosciences and Nutrition,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",1,0.57946,,0.08115,,0.91896,,0.72164,,50,,B,,usable mapping rate,legacy,early,unknown,random_priming,unknown,bulk,unknown,unknown,,Sweden,2011-06-09,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 8091,ERR034124,ERX012650,ERS032265,ERP000635,PRJEB2512,The Zebrafish transcriptome during early development,KI-BN-JKE-DRERIO-RNASEQ-2011,Transcriptome Analysis,Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions.,,,RNA extracted from zebrafish embryo at 1 cell stage,zebrafish embryo 1 cell,SAMEA791630,"Department of Biosciences and Nutrition, Karolinska Institutet, Sweden",ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen,,,,,,,,,Transcriptome profiling of early zebrafish development,KI BN JKE DRERIO RNASEQ 2011 1cell,JKE Drerio rna seq,Transcriptome profiling of 1 cell stage of zebrafish embryos.,Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems.,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ABI_SOLID,AB SOLiD System 3.0,500Application ReadForward1,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 36255,SRR062662,SRX025030,SRS085809,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,5.3hpf,GSM564432,,tissue:developing embryos|background:AB; wild type|developmental stage:post MBT stage embryo 5.3hpf,5.3hpf,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:post MBT stage embryo 5.3hpf,GSM564432,GSM564432: 5.3hpf,GSM564432: 5.3hpf,GSM564432: 5.3hpf,1,,GEO Accession:GSM564432,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,0Application ReadForward1,SRP003165,,,,,2778008350.0,55560167.0,GSM564432 1,0:50,,50,,,,,,,,,SRX025030,SRS085809,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.7379,,0.09683,,0.84751,,0.5252,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 36256,SRR062661,SRX025029,SRS085808,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,3.5hpf,GSM564431,,tissue:developing embryos|background:AB; wild type|developmental stage:MBT stage embryo 3.5hpf,3.5hpf,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:MBT stage embryo 3.5hpf,GSM564431,GSM564431: 3.5hpf,GSM564431: 3.5hpf,GSM564431: 3.5hpf,1,,GEO Accession:GSM564431,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,0Application ReadForward1,SRP003165,,,,,1894338450.0,37886769.0,GSM564431 1,0:50,,50,,,,,,,,,SRX025029,SRS085808,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.73958,,0.04864,,0.82378,,0.49728,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 36257,SRR062660,SRX025028,SRS085807,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,128/256 cells,GSM564430,,tissue:developing embryos|background:AB; wild type|developmental stage:mixure of 128/256 cell embryos,128/256 cells,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:mixure of 128/256 cell embryos,GSM564430,GSM564430: 128/256 cells,GSM564430: 128/256 cells,GSM564430: 128/256 cells,1,,GEO Accession:GSM564430,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,0Application ReadForward1,SRP003165,,,,,1355951300.0,27119026.0,GSM564430 1,0:50,,50,,,,,,,,,SRX025028,SRS085807,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.73373,,0.03657,,0.82773,,0.50091,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 36258,SRR062659,SRX025027,SRS085806,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,16/32 cells,GSM564429,,tissue:developing embryos|background:AB; wild type|developmental stage:mixure of 16/32 cell embryos,16/32 cells,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:mixure of 16/32 cell embryos,GSM564429,GSM564429: 16/32 cells,GSM564429: 16/32 cells,GSM564429: 16/32 cells,1,,GEO Accession:GSM564429,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,0Application ReadForward1,SRP003165,,,,,1792238300.0,35844766.0,GSM564429 1,0:50,,50,,,,,,,,,SRX025027,SRS085806,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.6993,,0.04019,,0.83763,,0.50284,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 36259,SRR062658,SRX025026,SRS085805,SRP003165,PRJNA127881,High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line,GSE22830,Transcriptome Analysis,mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf,,pubmed:21555364;pubmed:24586560;pubmed:23676078,,1 cell,GSM564428,,tissue:developing embryos|background:AB; wild type|developmental stage:just fertilized 1cell embryos,1 cell,ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters:  Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline.  Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.  A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.,developing embryos,Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.,mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.,Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.,background:AB; wild type|developmental stage:just fertilized 1cell embryos,GSM564428,GSM564428: 1 cell,GSM564428: 1 cell,GSM564428: 1 cell,1,,GEO Accession:GSM564428,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,0Application ReadForward1,SRP003165,,,,,1175348550.0,23506971.0,GSM564428 1,0:50,,50,,,,,,,,,SRX025026,SRS085805,SRA022850,GEO,"Computational and Systems Biology, Genome Institute of Singapore",1,0.75876,,0.05232,,0.86762,,0.50392,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Singapore,2010-07-08,Zygote,Embryo,Embryo Imprecise,All anatomical structures 36482,SRR530894,SRX172598,SRS352620,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 3,GSM979608,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979608,GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq,GSM979608 1,GSM979608: 60hpf TCDD 3,1,,GEO Accession:GSM979608,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,,,1007239870.0,28778282.0,GSM979608 r1,0:35,0:284531587;1:248579138;2:213782485;3:258771962;.:1574698,35,,,,,,,,,SRX172598,SRS352620,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04824,,0.03,,0.981,,0.49967,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36483,SRR530893,SRX172597,SRS352619,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 2,GSM979607,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979607,GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq,GSM979607 1,GSM979607: 60hpf TCDD 2,1,,GEO Accession:GSM979607,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0011.csfasta,SOLiD_native,407347325.0,11638495.0,GSM979607 r1,0:35,0:99062820;1:113921998;2:81336108;3:112422342;.:604057,35,,,,,,,,,SRX172597,SRS352619,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.04258,,0.02455,,0.98287,,0.5048,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36484,SRR530892,SRX172596,SRS352618,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf TCDD 1,GSM979606,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,60hpf TCDD 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD,GSM979606,GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq,GSM979606 1,GSM979606: 60hpf TCDD 1,1,,GEO Accession:GSM979606,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0010.csfasta,SOLiD_native,680837045.0,19452487.0,GSM979606 r1,0:35,0:165079839;1:167219862;2:147812329;3:199659766;.:1065249,35,,,,,,,,,SRX172596,SRS352618,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.02295,,0.01479,,0.98884,,0.55191,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36485,SRR530891,SRX172595,SRS352617,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 3,GSM979605,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979605,GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq,GSM979605 1,GSM979605: 60hpf DMSO 3,1,,GEO Accession:GSM979605,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0009.csfasta,SOLiD_native,495019840.0,14143424.0,GSM979605 r1,0:35,0:134854583;1:126192934;2:102458221;3:130747961;.:766141,35,,,,,,,,,SRX172595,SRS352617,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.06707,,0.04409,,0.97285,,0.5058,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36486,SRR530890,SRX172594,SRS352616,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 2,GSM979604,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979604,GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq,GSM979604 1,GSM979604: 60hpf DMSO 2,1,,GEO Accession:GSM979604,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0008.qual,SOLiD_native,440403425.0,12582955.0,GSM979604 r1,0:35,0:110302240;1:106481197;2:104551283;3:118415637;.:653068,35,,,,,,,,,SRX172594,SRS352616,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05778,,0.03522,,0.97423,,0.50884,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36487,SRR530889,SRX172593,SRS352615,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,60hpf DMSO 1,GSM979603,,source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,60hpf DMSO 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO,GSM979603,GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq,GSM979603 1,GSM979603: 60hpf DMSO 1,1,,GEO Accession:GSM979603,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0007.csfasta MH_0007.qual,SOLiD_native SOLiD_native,583800490.0,16680014.0,GSM979603 r1,0:35,0:166122108;1:149534173;2:111986455;3:155255262;.:902492,35,,,,,,,,,SRX172593,SRS352615,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.05644,,0.03829,,0.9781,,0.4997,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36488,SRR530888,SRX172592,SRS352614,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf TCDD 3,GSM979602,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,36hpf TCDD 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,GSM979602,GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq,GSM979602 1,GSM979602: 36hpf TCDD 3,1,,GEO Accession:GSM979602,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0006.qual MH_0006.csfasta,SOLiD_native SOLiD_native,214059615.0,6115989.0,GSM979602 r1,0:35,0:56635752;1:54053300;2:48355842;3:54677354;.:337367,35,,,,,,,,,SRX172592,SRS352614,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.13044,,0.07694,,0.95704,,0.53005,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36489,SRR530887,SRX172591,SRS352613,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf TCDD 2,GSM979601,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,36hpf TCDD 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,GSM979601,GSM979601: 36hpf TCDD 2; Danio rerio; RNA Seq,GSM979601 1,GSM979601: 36hpf TCDD 2,1,,GEO Accession:GSM979601,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,,,388475115.0,11099289.0,GSM979601 r1,0:35,0:103611863;1:99408831;2:86592980;3:98238344;.:623097,35,,,,,,,,,SRX172591,SRS352613,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.15634,,0.10763,,0.96069,,0.47755,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36490,SRR530886,SRX172590,SRS352612,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf TCDD 1,GSM979600,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,36hpf TCDD 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD,GSM979600,GSM979600: 36hpf TCDD 1; Danio rerio; RNA Seq,GSM979600 1,GSM979600: 36hpf TCDD 1,1,,GEO Accession:GSM979600,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0004.csfasta,SOLiD_native,366389765.0,10468279.0,GSM979600 r1,0:35,0:100797199;1:91391785;2:80412155;3:93217840;.:570786,35,,,,,,,,,SRX172590,SRS352612,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.14106,,0.09874,,0.95724,,0.49685,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36491,SRR530885,SRX172589,SRS352611,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf DMSO 3,GSM979599,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,36hpf DMSO 3,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,GSM979599,GSM979599: 36hpf DMSO 3; Danio rerio; RNA Seq,GSM979599 1,GSM979599: 36hpf DMSO 3,1,,GEO Accession:GSM979599,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0003.csfasta,SOLiD_native,2108864835.0,60253281.0,GSM979599 r1,0:35,0:591489585;1:461028640;2:379338654;3:673048278;.:3959678,35,,,,,,,,,SRX172589,SRS352611,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.09321,,0.06563,,0.98244,,0.50577,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36492,SRR530884,SRX172588,SRS352610,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf DMSO 2,GSM979598,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,36hpf DMSO 2,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,GSM979598,GSM979598: 36hpf DMSO 2; Danio rerio; RNA Seq,GSM979598 1,GSM979598: 36hpf DMSO 2,1,,GEO Accession:GSM979598,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0002.qual,SOLiD_native,363765885.0,10393311.0,GSM979598 r1,0:35,0:99316622;1:92947128;2:80099367;3:90839592;.:563176,35,,,,,,,,,SRX172588,SRS352610,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.13435,,0.09839,,0.96146,,0.49914,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36493,SRR530883,SRX172587,SRS352609,SRP014646,PRJNA171751,MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data],GSE39808,Transcriptome Analysis,Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing,parent bioproject:PRJNA171747,pubmed:22921993,,36hpf DMSO 1,GSM979597,,source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,36hpf DMSO 1,CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files,Embryos,,Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.,,strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO,GSM979597,GSM979597: 36hpf DMSO 1; Danio rerio; RNA Seq,GSM979597 1,GSM979597: 36hpf DMSO 1,1,,GEO Accession:GSM979597,RNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ABI_SOLID,AB SOLiD System 3.0,350Application ReadForward1,SRP014646,,,MH_0001F3.csfasta MH_0001F3_QV.qual,SOLiD_native SOLiD_native,309659000.0,8847400.0,GSM979597 r1,0:35,0:83729307;1:78100521;2:70827559;3:76531823;.:469790,35,,,,,,,,,SRX172587,SRS352609,SRA056525,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",1,0.56398,,0.33182,,0.91092,,0.5842,,35,,B,,usable mapping rate,legacy,early,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2012-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36685,SRR801688,SRX258168,SRS406299,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish 1 wpf larvae,GSM1112163: larva 1 week,GSM1112163,,strain:AB|developmental stage:larva 1 week|tissue:larva,larva 1 week,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish 1 wpf larvae,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:larva 1 week|tissue:larva,GSM1112163,GSM1112163: larva 1 week; Danio rerio; RNA Seq,GSM1112163 1,,1,,GEO Accession:GSM1112163,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_1week_F3.csfasta.bz2 D_rerio_1week_F3_QV.qual.bz2,SOLiD_native SOLiD_native,18866346300.0,377326926.0,GSM1112163 r1,0:50,0:4319577052;1:5210931849;2:5202393345;3:4013865803;.:119578251,50,,,,,,,,,SRX258168,SRS406299,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.60649,,0.05524,,0.86746,,0.51092,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Larval,Larval,Embryo Imprecise,All anatomical structures 36686,SRR801687,SRX258167,SRS406298,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Protruding mouth stage,GSM1112162: Protruding mouth 72hpf,GSM1112162,,strain:AB|developmental stage:Protruding mouth 72hpf|tissue:embryo,Protruding mouth 72hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Protruding mouth stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Protruding mouth 72hpf|tissue:embryo,GSM1112162,GSM1112162: Protruding mouth 72hpf; Danio rerio; RNA Seq,GSM1112162 1,,1,,GEO Accession:GSM1112162,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_72hpf_F3.csfasta.bz2 D_rerio_72hpf_F3_QV.qual.bz2,SOLiD_native SOLiD_native,19339397750.0,386787955.0,GSM1112162 r1,0:50,0:4755453154;1:5011845177;2:5110574744;3:4002085043;.:459439632,50,,,,,,,,,SRX258167,SRS406298,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.34099,,0.03045,,0.92409,,0.49783,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Larval,Larval,Embryo Imprecise,All anatomical structures 36687,SRR801685,SRX258166,SRS406297,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Pec fin stage,GSM1112161: Pec fin 60hpf,GSM1112161,,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,Pec fin 60hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Pec fin stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,GSM1112161,GSM1112161: Pec fin 60hpf; Danio rerio; RNA Seq,GSM1112161 1,,1,,GEO Accession:GSM1112161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_60hpf_rep1_F3_QV.qual.bz2 D_rerio_60hpf_rep1_F3.csfasta.bz2,SOLiD_native SOLiD_native,14061264450.0,281225289.0,GSM1112161 r1,0:50,0:3272552510;1:3838757055;2:3984098731;3:2865843173;.:100012981,50,,,,,,,,,SRX258166,SRS406297,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.64298,,0.04687,,0.8452,,0.50527,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36688,SRR801686,SRX258166,SRS406297,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Pec fin stage,GSM1112161: Pec fin 60hpf,GSM1112161,,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,Pec fin 60hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Pec fin stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Pec fin 60hpf|tissue:embryo,GSM1112161,GSM1112161: Pec fin 60hpf; Danio rerio; RNA Seq,GSM1112161 1,,1,,GEO Accession:GSM1112161,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_60hpf_rep2_F3.csfasta.bz2 D_rerio_60hpf_rep2_F3_QV.qual.bz2,SOLiD_native SOLiD_native,4988485300.0,99769706.0,GSM1112161 r2,0:50,0:1195740374;1:1346591727;2:1390300069;3:1024571482;.:31281648,50,,,,,,,,,SRX258166,SRS406297,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.65039,,0.04382,,0.84463,,0.50042,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36689,SRR801684,SRX258165,SRS406296,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Long pec stage,GSM1112160: Long pec 48hpf,GSM1112160,,strain:AB|developmental stage:Long pec 48hpf|tissue:embryo,Long pec 48hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Long pec stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Long pec 48hpf|tissue:embryo,GSM1112160,GSM1112160: Long pec 48hpf; Danio rerio; RNA Seq,GSM1112160 1,,1,,GEO Accession:GSM1112160,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_48hpf_F3.csfasta.bz2 D_rerio_48hpf_F3_QV.qual.bz2,SOLiD_native SOLiD_native,18932266250.0,378645325.0,GSM1112160 r1,0:50,0:4346139923;1:5132091383;2:5261012454;3:4060753494;.:132268996,50,,,,,,,,,SRX258165,SRS406296,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.59799,,0.03168,,0.87787,,0.49407,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Hatching,Embryo,Embryo Imprecise,All anatomical structures 36690,SRR801683,SRX258164,SRS406295,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the Prim 25 stage,GSM1112159: Prim 25 36hpf,GSM1112159,,strain:AB|developmental stage:Prim 25 36hpf|tissue:embryo,Prim 25 36hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the Prim 25 stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:Prim 25 36hpf|tissue:embryo,GSM1112159,GSM1112159: Prim 25 36hpf; Danio rerio; RNA Seq,GSM1112159 1,,1,,GEO Accession:GSM1112159,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_36hpf_F3.csfasta.bz2 D_rerio_36hpf_F3_QV.qual.bz2,SOLiD_native SOLiD_native,17101319300.0,342026386.0,GSM1112159 r1,0:50,0:3937246171;1:4674442353;2:4750820696;3:3639194318;.:99615762,50,,,,,,,,,SRX258164,SRS406295,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.64605,,0.05087,,0.86454,,0.49193,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 36691,SRR801682,SRX258163,SRS406294,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the 15 somite stage,GSM1112158: 15 somite 16.5 17.5hpf,GSM1112158,,strain:AB|developmental stage:15 somite 16.5 17.5hpf|tissue:embryo,15 somite 16.5 17.5hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the 15 somite stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:15 somite 16.5 17.5hpf|tissue:embryo,GSM1112158,GSM1112158: 15 somite 16.5 17.5hpf; Danio rerio; RNA Seq,GSM1112158 1,,1,,GEO Accession:GSM1112158,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_15somite_F3_QV.qual.bz2 D_rerio_15somite_F3.csfasta.bz2,SOLiD_native SOLiD_native,19881065650.0,397621313.0,GSM1112158 r1,0:50,0:4616309398;1:5374070017;2:5493789005;3:4261458107;.:135439123,50,,,,,,,,,SRX258163,SRS406294,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.65251,,0.04145,,0.8803,,0.49159,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 36692,SRR801681,SRX258162,SRS406293,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the 50% epiboly stage,GSM1112157: 50% epiboly 5.25hpf,GSM1112157,,strain:AB|developmental stage:50% epiboly 5.25hpf|tissue:embryo,50% epiboly 5.25hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the 50% epiboly stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:50% epiboly 5.25hpf|tissue:embryo,GSM1112157,GSM1112157: 50% epiboly 5.25hpf; Danio rerio; RNA Seq,GSM1112157 1,,1,,GEO Accession:GSM1112157,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_50epiboly_F3.csfasta.bz2 D_rerio_50epiboly_F3_QV.qual.bz2,SOLiD_native SOLiD_native,18813904400.0,376278088.0,GSM1112157 r1,0:50,0:4325556677;1:5167803890;2:5309373134;3:4011170699;.:0,50,,,,,,,,,SRX258162,SRS406293,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.6164,,0.05047,,0.89767,,0.50223,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 36693,SRR801680,SRX258161,SRS406292,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the oblong sphere stage,GSM1112156: oblong sphere 3.6 4hpf,GSM1112156,,strain:AB|developmental stage:oblong sphere 3.6 4hpf|tissue:embryo,oblong sphere 3.6 4hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the oblong sphere stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:oblong sphere 3.6 4hpf|tissue:embryo,GSM1112156,GSM1112156: oblong sphere 3.6 4hpf; Danio rerio; RNA Seq,GSM1112156 1,,1,,GEO Accession:GSM1112156,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_oblong_sphere_F3.csfasta.bz2 D_rerio_oblong_sphere_F3_QV.qual.bz2,SOLiD_native SOLiD_native,16938508000.0,338770160.0,GSM1112156 r1,0:50,0:3947082853;1:4563069432;2:4709732005;3:3599468311;.:119155399,50,,,,,,,,,SRX258161,SRS406292,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.60716,,0.02545,,0.85186,,0.48927,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Blastula,Embryo,Embryo Imprecise,All anatomical structures 36694,SRR801679,SRX258160,SRS406291,SRP020469,PRJNA195909,RNA sequencing project for zebrafish embryo and larva development,GSE45706,Transcriptome Analysis,Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes yet large gaps still remain in the functional pathways critical for each developmental stage especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish,,pubmed:23700457;pubmed:26891128,source: Zebrafish embryos at the 64 cell stage,GSM1112155: 64 cell 2 hpf,GSM1112155,,strain:AB|developmental stage:64 cell 2 hpf|tissue:embryo,64 cell 2 hpf,Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly,Zebrafish embryos at the 64 cell stage,Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.,Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad CA USA methods according to the manufacturer’s instruction. RNA quality was evaluated by gel electrophoresis and the concentration was measured with NanoDrop 2000 Thermo Scientific，Waltham MA USA.The aliquots were stored at 80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second The ribosomal RNA removal steps were replaced by two rounds of polyA purification with the first round using the PolyATtract® mRNA Isolation Systems Promega Madison WI USA and the second round using the PolyAPurist™ Kit Ambion Austin TX USA. About 0.8 μg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen Carlsbad CA USA and 100–200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.,Zebrafish embryos and larvae were collected and maintained at approximately 28.5°C and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995,strain:AB|developmental stage:64 cell 2 hpf|tissue:embryo,GSM1112155,GSM1112155: 64 cell 2 hpf; Danio rerio; RNA Seq,GSM1112155 1,,1,,GEO Accession:GSM1112155,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP020469,,,D_rerio_64cell_F3.csfasta.bz2 D_rerio_64cell_F3_QV.qual.bz2,SOLiD_native SOLiD_native,11793112050.0,235862241.0,GSM1112155 r1,0:50,0:2729453191;1:3189868180;2:3325229431;3:2482063391;.:66497857,50,,,,,,,,,SRX258160,SRS406291,SRA072427,GEO,Shanghai Chenshan Botanical Garden,1,0.56575,,0.01697,,0.8538,,0.48681,,50,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2013-04-02,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 37907,SRR1104969,SRX424037,SRS527958,SRP035264,PRJNA236557,Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq],GSE53758,Transcriptome Analysis,To determine the global impact of the clbn mutation on gene expression and efficiency of U2 and U12 type splicing we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each genotyped homozygous wildtype and homozygous clbns841 mutants respectively,parent bioproject:PRJNA236230,pubmed:24516132,,108hpf clbn,GSM1303831,,source name:108hpf clbn larvae|genotype/variation:clbns841|development stage:108 hpf|tissue:whole larvae,108hpf clbn,50bp single end reads were mapped using the X MATE recursive mapping pipeline 42 allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9,108hpf clbn larvae,Starting at 24 hpf embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation,Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.,Embryos for all experiments were produced by natural spawning transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5°C incubator on a 12h light/dark cycle.,genotype/variation:clbns841|developmental stage:108 hpf|tissue:whole larvae,GSM1303831,GSM1303831: 108hpf clbn; Danio rerio; RNA Seq,GSM1303831,,1,Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.,GEO Accession:GSM1303831,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP035264,,,108hpf_clbn_F3_QV.qual.bz2 108hpf_clbn_F3.csfasta.bz2,SOLiD_native SOLiD_native,2698882700.0,53977654.0,GSM1303831 r1,0:50,0:653022205;1:711705790;2:753066133;3:571973990;.:9114582,50,,,,,,,,,SRX424037,SRS527958,SRA123959,GEO,"Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research",1,0.56134,,0.05842,,0.84303,,0.49093,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Australia,2014-01-09,Larval,Larval,Whole Organism,All anatomical structures 37908,SRR1104968,SRX424036,SRS527957,SRP035264,PRJNA236557,Genome wide analysis of gene expression and intron retention during development in a U12 type splicing deficient zebrafish mutant [RNA seq],GSE53758,Transcriptome Analysis,To determine the global impact of the clbn mutation on gene expression and efficiency of U2 and U12 type splicing we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2 type and U12 type intron on a genome wide scale to confirm that rnpc3 deficiency specifically impairs U12 type splicing. RNAseq and microarray data were combined to yield high confidence lists of differentially expressed genes which show that impaired U12 type splicing has a wide ranging effect on the developing transcriptome. Overall design: RNAseq libraries prepared from 108 hpf zebrafish larvae approx. 60 embryos each genotyped homozygous wildtype and homozygous clbns841 mutants respectively,parent bioproject:PRJNA236230,pubmed:24516132,,108hpf wt,GSM1303830,,source name:108hpf wt larvae|genotype/variation:wildtype|development stage:108 hpf|tissue:whole larvae,108hpf wt,50bp single end reads were mapped using the X MATE recursive mapping pipeline 42 allowing for 5 color space mismatches per 50bp read CS 50 5 The uniquely mappable regions uniqueome of the ZV9 assembly were calculated using the same mapping parameters CS 50 5 For intron retention analysis RPKM were calculated for annotated Refseq introns + manually annotated U12 type introns using Galaxy For gene expression analysis RPKM were calculated for annotated Refseq coding regions using Galaxy Genome build: Zebrafish Zv9,108hpf wt larvae,Starting at 24 hpf embryos were transferred into egg water containing 0.003% 1 Phenyl 2 thiourea PTU to prevent pigmentation,Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.,Embryos for all experiments were produced by natural spawning transferred into petri dishes with pre warmed egg water 60mg of sea salt/1L ddH20 and placed in a 28.5°C incubator on a 12h light/dark cycle.,genotype/variation:wildtype|developmental stage:108 hpf|tissue:whole larvae,GSM1303830,GSM1303830: 108hpf wt; Danio rerio; RNA Seq,GSM1303830,,1,Genomic DNA and total RNA were extracted concurrently form single embryos by acid guanidinium thiocyanate phenol chloroform extraction. Genomic DNA extraction and genotyping of individual embryos was completed first and aqueous phases of all homozygous wildtype and mutant larvae respectively were pooled prior to RNA precipiation with isopropanol. For RNA sequencing RNA was extracted from approx 60 pooled genotyped larvae and subsequently enriched for polyA RNA by two successive rounds of polyA selection with the MicroPolyAPurist Kit Ambion. Libraries for deep sequencing were generated using the SOLiD™ Whole Transcriptome Analysis Kit with protocol Part Number 4409491 Rev F 08/2009. 8μl of polyA RNA were was fragmented by incubating with RNase III for 10min at 37°C and immediately purified on Qiagen RNeasy columns. Samples were eluted in 50μl of nuclease free water and the columns incubated for 10min before the final centrifugation. Samples were concentrated to a volume of 5μl by centrifuging under vacuum at 40°C. 1μl of each sample was analysed on the Agilent Bioanalyzer Agilent using an RNA Nano 6000 chip Agilent to assess quantity and size distribution of the fragmented RNA. The fragmented RNA was hybridised and ligated to Adaptor Mix A to generate templates for SOLiD System sequencing from the 5’ end of the sense strand. post o/n ligation samples were reverse transcribed for 30min at 42°C and the obtained cDNA purified using Qiagen inElute PCR Purification Kit. 100 200bp fragments were size selected by excision from a 6% polyacrylamide 8M urea TBE gels. cDNA in gel slices was subjected to 18 cycles of amplification and purified using PureLink PCR Micro columns Invitrogen. The majority of cDNAs in the library was between 150 and 250bp in size and less than 2 8% of cDNAs fell in the 25 150bp size range as per protocol requirements. The finished cDNA libraries were used for attachment to beads by emulsion PCR.,GEO Accession:GSM1303830,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP035264,,,108hpf_wt_F3_QV.qual.bz2 108hpf_wt_F3.csfasta.bz2,SOLiD_native SOLiD_native,2835473700.0,56709474.0,GSM1303830 r1,0:50,0:697915785;1:748317376;2:781024795;3:605838541;.:2377203,50,,,,,,,,,SRX424036,SRS527957,SRA123959,GEO,"Heath Laboratory, Development and Cancer, Walter and Eliza Hall Institute of Medical Research",1,0.57033,,0.05759,,0.8384,,0.49692,,50,,B,,usable mapping rate,legacy,early,full_length,poly_a,unknown,bulk,unknown,unknown,,Australia,2014-01-09,Larval,Larval,Whole Organism,All anatomical structures