run_metadata
86 rows where experiment.library_source = "TRANSCRIPTOMIC" and experiment.platform = "ABI_SOLID"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8088 | 8088 | ERR034127 | ERX012653 | ERS032268 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 50% epiboly stage | zebrafish embryo 50 epiboly | SAMEA791629 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 50epiboly | JKE Drerio rna seq | Transcriptome profiling of 50% epiboly stages of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz | SOLiD_native SOLiD_native | 3929903550.0 | 78598071.0 | KI BN JKE DRERIO RNASEQ 2011 50epiboly | 0:50 | 50 | ERX012653 | ERS032268 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.60757 | 0.09893 | 0.94899 | 0.77821 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8089 | 8089 | ERR034126 | ERX012652 | ERS032267 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 512 cell stage | zebrafish embryo 512 cell | SAMEA791632 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 512cell | JKE Drerio rna seq | Transcriptome profiling of 512 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz | SOLiD_native SOLiD_native | 3918756250.0 | 78375125.0 | KI BN JKE DRERIO RNASEQ 2011 512cell | 0:50 | 50 | ERX012652 | ERS032267 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.63824 | 0.09111 | 0.91969 | 0.73496 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8090 | 8090 | ERR034125 | ERX012651 | ERS032266 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 16 cell stage | zebrafish embryo 16 cell | SAMEA791631 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 16cell | JKE Drerio rna seq | Transcriptome profiling of 16 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz | SOLiD_native SOLiD_native | 4256756500.0 | 85135130.0 | KI BN JKE DRERIO RNASEQ 2011 16cell | 0:50 | 50 | ERX012651 | ERS032266 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.57946 | 0.08115 | 0.91896 | 0.72164 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Cleavage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8091 | 8091 | ERR034124 | ERX012650 | ERS032265 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 1 cell stage | zebrafish embryo 1 cell | SAMEA791630 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 1cell | JKE Drerio rna seq | Transcriptome profiling of 1 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz | SOLiD_native SOLiD_native | 3676380950.0 | 73527619.0 | KI BN JKE DRERIO RNASEQ 2011 1cell | 0:50 | 50 | ERX012650 | ERS032265 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.64855 | 0.08432 | 0.9052 | 0.74223 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 24546 | 24546 | ERR964671 | ERX1041634 | ERS792101 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484816 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2625510200.0 | 52510204.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 | 0:50 | 0:677149824;1:606769571;2:761187530;3:578170290;.:2232985 | 50 | ERX1041634 | ERS792101 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.71662 | 0.0994 | 0.91644 | 0.74578 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Zygote | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24547 | 24547 | ERR964670 | ERX1041633 | ERS792104 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484819 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5325942150.0 | 106518843.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 | 0:50 | 0:1376469323;1:1227617853;2:1499234750;3:1210700143;.:11920081 | 50 | ERX1041633 | ERS792104 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.7059 | 0.10511 | 0.91492 | 0.75125 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Gastrula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24548 | 24548 | ERR964669 | ERX1041632 | ERS792103 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484818 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5452772750.0 | 109055455.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 | 0:50 | 0:1391108289;1:1312099760;2:1551659810;3:1179923010;.:17981881 | 50 | ERX1041632 | ERS792103 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.73133 | 0.07897 | 0.88057 | 0.63645 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Blastula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24549 | 24549 | ERR964667 | ERX1041630 | ERS792101 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484816 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5717685400.0 | 114353708.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 | 0:50 | 0:1643444976;1:1261570333;2:1504304496;3:1282815913;.:25549682 | 50 | ERX1041630 | ERS792101 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.72274 | 0.11151 | 0.92348 | 0.71904 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Zygote | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24550 | 24550 | ERR964668 | ERX1041631 | ERS792102 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484817 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5278508300.0 | 105570166.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2 | 0:50 | 0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869 | 50 | ERX1041631 | ERS792102 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.71371 | 0.09346 | 0.91539 | 0.73015 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Cleavage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24551 | 24551 | ERR964674 | ERX1041637 | ERS792104 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484819 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2541596650.0 | 50831933.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 | 0:50 | 0:670988333;1:585266057;2:708634642;3:574052618;.:2655000 | 50 | ERX1041637 | ERS792104 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.72135 | 0.10529 | 0.90997 | 0.76049 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Gastrula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24552 | 24552 | ERR964673 | ERX1041636 | ERS792103 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484818 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2027760000.0 | 40555200.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 | 0:50 | 0:511413081;1:492642968;2:594959353;3:426692118;.:2052480 | 50 | ERX1041636 | ERS792103 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.77106 | 0.08154 | 0.85675 | 0.64875 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Blastula | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 24553 | 24553 | ERR964672 | ERX1041635 | ERS792102 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484817 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 2719433200.0 | 54388664.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 | 0:50 | 0:699731678;1:628745158;2:754903505;3:633574679;.:2478180 | 50 | ERX1041635 | ERS792102 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.73214 | 0.09566 | 0.90836 | 0.74043 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Cleavage | Embryo | Undetermined | Embryo Imprecise | |||||||||||||||||||||||||||||
| 36255 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | ||||||||||||||||||||||||
| 36260 | 36260 | SRR062657 | SRX025025 | SRS085804 | 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 | Maternal | GSM564427 | tissue:Unfertilized egg|background:AB; wild type|developmental stage:unfertilized eggs | Maternal | 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. | Unfertilized egg | 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:unfertilized eggs | GSM564427 | GSM564427: Maternal | GSM564427: Maternal | GSM564427: Maternal | 1 | GEO Accession:GSM564427 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP003165 | 1566199300.0 | 31323986.0 | GSM564427 1 | 0:50 | 50 | SRX025025 | SRS085804 | SRA022850 | GEO | Computational and Systems Biology, Genome Institute of Singapore | 1 | 0.72688 | 0.05657 | 0.876 | 0.51223 | 50 | B | usable mapping rate | legacy | early | full_length | poly_a | unknown | bulk | unknown | unknown | Singapore | 2010-07-08 | Zygote | Embryo | Oocyte | Reproductive System | ||||||||||||||||||||||||
| 36336 | 36336 | SRR390721 | SRX112005 | SRS282726 | SRP009863 | PRJNA151317 | A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver | GSE34493 | Transcriptome Analysis | We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age. | mRNA from HBx+HCP transgenic line | GSM850201 | source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver | mRNA from HBx+HCP transgenic line | HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. | zebrafish liver | Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis | The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. | Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. | phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver | GSM850201 | GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq | GSM850201 1 | GSM850201: mRNA from HBx+HCP transgenic line | 1 | GEO Accession:GSM850201 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP009863 | HBx+HCP.qual HBx+HCP.csfasta | SOLiD_native SOLiD_native | 3946087000.0 | 78921740.0 | GSM850201 r1 | 0:50 | 0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394 | 50 | SRX112005 | SRS282726 | SRA048698 | GEO | Institute of Cellular and Organismic Biology, Academia Sinica | 1 | 0.71816 | 0.05681 | 0.91727 | 0.25279 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Taiwan | 2011-12-16 | Undetermined | Adult | Liver | Liver and Biliary System | ||||||||||||||||||||||
| 36337 | 36337 | SRR390720 | SRX112004 | SRS282725 | SRP009863 | PRJNA151317 | A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver | GSE34493 | Transcriptome Analysis | We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age. | mRNA from HCP transgenic line | GSM850200 | source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver | mRNA from HCP transgenic line | HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. | zebrafish liver | Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis | The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. | Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. | phenotype:n1|strain:HCP transgenic|tissue:liver | GSM850200 | GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq | GSM850200 1 | GSM850200: mRNA from HCP transgenic line | 1 | GEO Accession:GSM850200 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP009863 | HCP.qual HCP.csfasta | SOLiD_native SOLiD_native | 4104044600.0 | 82080892.0 | GSM850200 r1 | 0:50 | 0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070 | 50 | SRX112004 | SRS282725 | SRA048698 | GEO | Institute of Cellular and Organismic Biology, Academia Sinica | 1 | 0.70132 | 0.05286 | 0.94422 | 0.26785 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Taiwan | 2011-12-16 | Undetermined | Adult | Liver | Liver and Biliary System | ||||||||||||||||||||||
| 36338 | 36338 | SRR390719 | SRX112003 | SRS282724 | SRP009863 | PRJNA151317 | A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver | GSE34493 | Transcriptome Analysis | We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age. | mRNA from HBx transgenic line | GSM850199 | source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver | mRNA from HBx transgenic line | HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. | zebrafish liver | Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis | The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. | Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. | phenotype:n1|strain:HBx transgenic|tissue:liver | GSM850199 | GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq | GSM850199 1 | GSM850199: mRNA from HBx transgenic line | 1 | GEO Accession:GSM850199 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP009863 | HBx.qual HBx.csfasta | SOLiD_native SOLiD_native | 3783924950.0 | 75678499.0 | GSM850199 r1 | 0:50 | 0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987 | 50 | SRX112003 | SRS282724 | SRA048698 | GEO | Institute of Cellular and Organismic Biology, Academia Sinica | 1 | 0.70675 | 0.04174 | 0.94146 | 0.22954 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Taiwan | 2011-12-16 | Undetermined | Adult | Liver | Liver and Biliary System | ||||||||||||||||||||||
| 36339 | 36339 | SRR390718 | SRX112002 | SRS282723 | SRP009863 | PRJNA151317 | A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver | GSE34493 | Transcriptome Analysis | We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age. | mRNA from AB strain | GSM850198 | source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver | mRNA from AB strain | WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. | zebrafish liver | Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis | The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. | Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. | phenotype:n1|strain:AB|tissue:liver | GSM850198 | GSM850198: mRNA from AB strain; Danio rerio; RNA Seq | GSM850198 1 | GSM850198: mRNA from AB strain | 1 | GEO Accession:GSM850198 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP009863 | WT.csfasta WT.qual | SOLiD_native SOLiD_native | 5129652800.0 | 102593056.0 | GSM850198 r1 | 0:50 | 0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426 | 50 | SRX112002 | SRS282723 | SRA048698 | GEO | Institute of Cellular and Organismic Biology, Academia Sinica | 1 | 0.73072 | 0.04843 | 0.95574 | 0.21796 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Taiwan | 2011-12-16 | Undetermined | Adult | Liver | Liver and Biliary System | ||||||||||||||||||||||
| 36482 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | 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 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | 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 | ||||||||||||||||||||||
| 36506 | 36506 | SRR566696 | SRX185761 | SRS361914 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: liver tumor M+D+ | GSM1000561: M+D+ 2 | GSM1000561 | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline | M+D+ 2 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor M+D+ | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline | GSM1000561 | GSM1000561: M+D+ 2; Danio rerio; RNA Seq | GSM1000561 1 | 1 | GEO Accession:GSM1000561 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M+D+_2_QV.qual M+D+_2.csfasta | SOLiD_native SOLiD_native | 1493416960.0 | 42669056.0 | GSM1000561 r1 | 0:35 | 0:377247910;1:348861020;2:522134600;3:237405266;.:7768164 | 35 | SRX185761 | SRS361914 | SRA058618 | GEO | National University of Singapore | 1 | 0.06244 | 0.00306 | 0.99567 | 0.34618 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36507 | 36507 | SRR566695 | SRX185760 | SRS361913 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: liver tumor M+D+ | GSM1000560: M+D+ 1 | GSM1000560 | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline | M+D+ 1 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor M+D+ | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline | GSM1000560 | GSM1000560: M+D+ 1; Danio rerio; RNA Seq | GSM1000560 1 | 1 | GEO Accession:GSM1000560 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | 1291539515.0 | 36901129.0 | GSM1000560 r1 | 0:35 | 0:266006021;1:328523841;2:440474617;3:254266912;.:2268124 | 35 | SRX185760 | SRS361913 | SRA058618 | GEO | National University of Singapore | 1 | 0.10629 | 0.0044 | 0.99239 | 0.31953 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||||
| 36508 | 36508 | SRR566694 | SRX185759 | SRS361912 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M D+ | GSM1000559: M D+ 2 | GSM1000559 | genotype:wildtype|tissue:liver|treatment:doxycycline | M D+ 2 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M D+ | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:wildtype|tissue:liver|treatment:doxycycline | GSM1000559 | GSM1000559: M D+ 2; Danio rerio; RNA Seq | GSM1000559 1 | 1 | GEO Accession:GSM1000559 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M-D+_2_QV.qual | SOLiD_native | 1438423910.0 | 41097826.0 | GSM1000559 r1 | 0:35 | 0:353104627;1:349496969;2:433338629;3:275089557;.:27394128 | 35 | SRX185759 | SRS361912 | SRA058618 | GEO | National University of Singapore | 1 | 0.04748 | 0.00442 | 0.99425 | 0.53794 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36509 | 36509 | SRR566693 | SRX185758 | SRS361911 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M D+ | GSM1000558: M D+ 1 | GSM1000558 | genotype:wildtype|tissue:liver|treatment:doxycycline | M D+ 1 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M D+ | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:wildtype|tissue:liver|treatment:doxycycline | GSM1000558 | GSM1000558: M D+ 1; Danio rerio; RNA Seq | GSM1000558 1 | 1 | GEO Accession:GSM1000558 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M-D+_1.csfasta | SOLiD_native | 1284638285.0 | 36703951.0 | GSM1000558 r1 | 0:35 | 0:328871758;1:317693850;2:402981931;3:233637468;.:1453278 | 35 | SRX185758 | SRS361911 | SRA058618 | GEO | National University of Singapore | 1 | 0.10539 | 0.00562 | 0.99141 | 0.37635 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36510 | 36510 | SRR566692 | SRX185757 | SRS361910 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M+D | GSM1000557: M+D 2 | GSM1000557 | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 | M+D 2 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M+D | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 | GSM1000557 | GSM1000557: M+D 2; Danio rerio; RNA Seq | GSM1000557 1 | 1 | GEO Accession:GSM1000557 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M+D-_2_QV.qual | SOLiD_native | 1404966080.0 | 40141888.0 | GSM1000557 r1 | 0:35 | 0:371691603;1:354481639;2:405221861;3:271978812;.:1592165 | 35 | SRX185757 | SRS361910 | SRA058618 | GEO | National University of Singapore | 1 | 0.07869 | 0.00455 | 0.99253 | 0.51508 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36511 | 36511 | SRR566691 | SRX185756 | SRS361909 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M+D | GSM1000556: M+D 1 | GSM1000556 | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 | M+D 1 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M+D | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 | GSM1000556 | GSM1000556: M+D 1; Danio rerio; RNA Seq | GSM1000556 1 | 1 | GEO Accession:GSM1000556 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M+D-_1_QV.qual M+D-_1.csfasta | SOLiD_native SOLiD_native | 1286706820.0 | 36763052.0 | GSM1000556 r1 | 0:35 | 0:252864341;1:338709089;2:436928155;3:256235022;.:1970213 | 35 | SRX185756 | SRS361909 | SRA058618 | GEO | National University of Singapore | 1 | 0.12399 | 0.00617 | 0.98752 | 0.50351 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36512 | 36512 | SRR566690 | SRX185755 | SRS361908 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M D | GSM1000555: M D 2 | GSM1000555 | genotype:wildtype|tissue:liver|treatment:n1 | M D 2 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M D | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:wildtype|tissue:liver|treatment:n1 | GSM1000555 | GSM1000555: M D 2; Danio rerio; RNA Seq | GSM1000555 1 | 1 | GEO Accession:GSM1000555 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M-D-_2_QV.qual M-D-_2.csfasta | SOLiD_native SOLiD_native | 1337952770.0 | 38227222.0 | GSM1000555 r1 | 0:35 | 0:391863829;1:347720340;2:312814682;3:283542736;.:2011183 | 35 | SRX185755 | SRS361908 | SRA058618 | GEO | National University of Singapore | 1 | 0.04605 | 0.00365 | 0.99494 | 0.51825 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36513 | 36513 | SRR566689 | SRX185754 | SRS361907 | SRP015680 | PRJNA174800 | Transcriptomic analyses of Myc induced zebrafish liver cancer | GSE40745 | Transcriptome Analysis | To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system. | pubmed:23038063 | source: control liver M D | GSM1000554: M D 1 | GSM1000554 | genotype:wildtype|tissue:liver|treatment:n1 | M D 1 | The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver M D | Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. | Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype:wildtype|tissue:liver|treatment:n1 | GSM1000554 | GSM1000554: M D 1; Danio rerio; RNA Seq | GSM1000554 1 | 1 | GEO Accession:GSM1000554 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP015680 | M-D-_1.csfasta | SOLiD_native | 1395143680.0 | 39861248.0 | GSM1000554 r1 | 0:35 | 0:439852883;1:355203725;2:298639546;3:299770820;.:1676706 | 35 | SRX185754 | SRS361907 | SRA058618 | GEO | National University of Singapore | 1 | 0.02094 | 0.00123 | 0.99784 | 0.58426 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2012-09-10 | Larval | Larval | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 36685 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | ||||||||||||||||||||||
| 36739 | 36739 | SRR867022 | SRX286270 | SRS420566 | SRP022549 | PRJNA202401 | Danio rerio Transcriptome or Gene expression | PRJNA202401 | Other | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish. | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish | General Sample for Danio rerio | ICH | strain:wild type | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish Bcat | Danio rerio boot | 1 | RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry. | RNA-Seq | TRANSCRIPTOMIC | unspecified | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP022549 | s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta | SOLiD_native SOLiD_native | 9801985250.0 | 196039705.0 | Zebrafish DV patterning Boot | 0:50 | 0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939 | 50 | SRX286270 | SRS420566 | SRA075737 | BAYGEN|NGSP | BAYGEN | 1 | 0.59289 | 0.09435 | 0.92669 | 0.7658 | 50 | B | usable mapping rate | legacy | early | 3prime | rrna_depletion | unknown | bulk | unknown | unknown | Hungary | 2013-05-23 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||||||||||||||||||||
| 36740 | 36740 | SRR867023 | SRX286271 | SRS420566 | SRP022549 | PRJNA202401 | Danio rerio Transcriptome or Gene expression | PRJNA202401 | Other | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish. | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish | General Sample for Danio rerio | ICH | strain:wild type | Full transcriptome analysis of early dorsoventral DV patterning in zebrafish ICH | Danio rerio ICH | 1 | RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry. | RNA-Seq | TRANSCRIPTOMIC | unspecified | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP022549 | s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual | SOLiD_native SOLiD_native | 10810535400.0 | 216210708.0 | Zebrafish DV patterning ICH | 0:50 | 0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417 | 50 | SRX286271 | SRS420566 | SRA075737 | BAYGEN|NGSP | BAYGEN | 1 | 0.42474 | 0.06136 | 0.93434 | 0.75757 | 50 | B | usable mapping rate | legacy | early | 3prime | rrna_depletion | unknown | bulk | unknown | unknown | Hungary | 2013-05-23 | Undetermined | Undetermined | Undetermined | Undetermined | ||||||||||||||||||||||||||||||
| 37108 | 37108 | SRR924082 | SRX316721 | SRS472258 | SRP026400 | PRJNA210007 | Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver | GSE48427 | Transcriptome Analysis | In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system. | pubmed:24176670;pubmed:23922661 | H2O treated zebrafish liver | GSM1177837 | source name:liver control|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control | H2O treated zebrafish liver | The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM. | liver control | 3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day. | Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control | GSM1177837 | GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq | GSM1177837 | 1 | Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | GEO Accession:GSM1177837 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP026400 | solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual | SOLiD_native SOLiD_native | 477311205.0 | 13637463.0 | GSM1177837 r1 | 0:35 | 0:176467601;1:101093405;2:105775125;3:93265462;.:709612 | 35 | SRX316721 | SRS472258 | SRA091803 | GEO | National University of Singapore | 1 | 0.02019 | 0.01385 | 0.9973 | 0.64062 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-06-28 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37109 | 37109 | SRR924081 | SRX316720 | SRS454027 | SRP026400 | PRJNA210007 | Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver | GSE48427 | Transcriptome Analysis | In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system. | pubmed:24176670;pubmed:23922661 | Arsenic treated zebrafish liver | GSM1177836 | source name:liver arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium | Arsenic treated zebrafish liver | The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM. | liver arsenic | 3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day. | Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium | GSM1177836 | GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq | GSM1177836 | 1 | Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. | GEO Accession:GSM1177836 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP026400 | solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta | SOLiD_native SOLiD_native | 477279215.0 | 13636549.0 | GSM1177836 r1 | 0:35 | 0:135280436;1:121477647;2:102046207;3:117826846;.:648079 | 35 | SRX316720 | SRS454027 | SRA091803 | GEO | National University of Singapore | 1 | 0.0161 | 0.00302 | 0.99334 | 0.51629 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-06-28 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37130 | 37130 | SRR952910 | SRX335554 | SRS470625 | SRP028848 | PRJNA215326 | Transcriptomic analyses of TCDD treated zebrafish liver | GSE49915 | Transcriptome Analysis | To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system | pubmed:24204792 | DMSO | GSM1209643 | source name:liver|tissue:liver|genotype:wildtype sibling|treatment:DMSO | DMSO | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM. | liver | 3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day. | Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:wildtype sibling|treatment:DMSO | GSM1209643 | GSM1209643: DMSO; Danio rerio; RNA Seq | GSM1209643 | 1 | Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1209643 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP028848 | solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual | SOLiD_native SOLiD_native | 409327205.0 | 11695063.0 | GSM1209643 r1 | 0:35 | 0:136723730;1:95263220;2:87949986;3:88818989;.:571280 | 35 | SRX335554 | SRS470625 | SRA098000 | GEO | National University of Singapore | 1 | 0.01735 | 0.00647 | 0.9946 | 0.51324 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-08-15 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37131 | 37131 | SRR952909 | SRX335553 | SRS470624 | SRP028848 | PRJNA215326 | Transcriptomic analyses of TCDD treated zebrafish liver | GSE49915 | Transcriptome Analysis | To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system | pubmed:24204792 | TCDD | GSM1209642 | source name:liver|tissue:liver|genotype:wildtype sibling|treatment:TCDD | TCDD | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM. | liver | 3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day. | Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:wildtype sibling|treatment:TCDD | GSM1209642 | GSM1209642: TCDD; Danio rerio; RNA Seq | GSM1209642 | 1 | Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1209642 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP028848 | solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta | SOLiD_native SOLiD_native | 627514895.0 | 17928997.0 | GSM1209642 r1 | 0:35 | 0:214639659;1:142538233;2:131819822;3:137625000;.:892181 | 35 | SRX335553 | SRS470624 | SRA098000 | GEO | National University of Singapore | 1 | 0.01773 | 0.00917 | 0.99646 | 0.56398 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-08-15 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37271 | 37271 | SRR1050719 | SRX392663 | SRS515660 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X+M D+ | GSM1289483 | source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline | X+M D+ | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline | GSM1289483 | GSM1289483: X+M D+; Danio rerio; RNA Seq | GSM1289483 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289483 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X+M-D+.csfasta.gz X+M-D+.qual | SOLiD_native SOLiD_native | 367532585.0 | 10500931.0 | GSM1289483 r1 | 0:35 | 0:113917936;1:90770860;2:74839037;3:87267038;.:737714 | 35 | SRX392663 | SRS515660 | SRA117588 | GEO | National University of Singapore | 1 | 0.03142 | 0.01041 | 0.99115 | 0.47722 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37272 | 37272 | SRR1050718 | SRX392662 | SRS515661 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X M+D+ | GSM1289482 | source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline | X M+D+ | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline | GSM1289482 | GSM1289482: X M+D+; Danio rerio; RNA Seq | GSM1289482 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289482 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X-M+D+.csfasta.gz X-M+D+.qual | SOLiD_native SOLiD_native | 524940885.0 | 14998311.0 | GSM1289482 r1 | 0:35 | 0:177873348;1:126792787;2:107434769;3:111636161;.:1203820 | 35 | SRX392662 | SRS515661 | SRA117588 | GEO | National University of Singapore | 1 | 0.04433 | 0.02519 | 0.99456 | 0.5443 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37273 | 37273 | SRR1050717 | SRX392661 | SRS515658 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X M D+ | GSM1289481 | source name:control liver|tissue:liver|genotype:wildtype sibling|agent:doxycycline | X M D+ | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:wildtype sibling|agent:doxycycline | GSM1289481 | GSM1289481: X M D+; Danio rerio; RNA Seq | GSM1289481 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289481 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X-M-D+.csfasta.gz X-M-D+.qual | SOLiD_native SOLiD_native | 503677265.0 | 14390779.0 | GSM1289481 r1 | 0:35 | 0:153190412;1:124381654;2:106372352;3:118615876;.:1116971 | 35 | SRX392661 | SRS515658 | SRA117588 | GEO | National University of Singapore | 1 | 0.03136 | 0.01201 | 0.99356 | 0.49598 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37274 | 37274 | SRR1050716 | SRX392660 | SRS515659 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X+M D | GSM1289480 | source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1 | X+M D | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1 | GSM1289480 | GSM1289480: X+M D ; Danio rerio; RNA Seq | GSM1289480 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289480 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X+M-D-.csfasta.gz X+M-D-.qual | SOLiD_native SOLiD_native | 634523960.0 | 18129256.0 | GSM1289480 r1 | 0:35 | 0:234010528;1:135057441;2:132344184;3:131577105;.:1534702 | 35 | SRX392660 | SRS515659 | SRA117588 | GEO | National University of Singapore | 1 | 0.06814 | 0.05142 | 0.99579 | 0.6174 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37275 | 37275 | SRR1050715 | SRX392659 | SRS515657 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X M+D | GSM1289479 | source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1 | X M+D | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1 | GSM1289479 | GSM1289479: X M+D ; Danio rerio; RNA Seq | GSM1289479 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289479 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X-M+D-.csfasta.gz X-M+D-.qual | SOLiD_native SOLiD_native | 417548565.0 | 11929959.0 | GSM1289479 r1 | 0:35 | 0:114209112;1:103552786;2:91302789;3:107590004;.:893874 | 35 | SRX392659 | SRS515657 | SRA117588 | GEO | National University of Singapore | 1 | 0.02253 | 0.00519 | 0.99218 | 0.61466 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37276 | 37276 | SRR1050714 | SRX392658 | SRS515656 | SRP034513 | PRJNA231764 | Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer | GSE53342 | Transcriptome Analysis | To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system | pubmed:24633177 | X M D | GSM1289478 | source name:control liver|tissue:liver|genotype:wildtype sibling|agent:n1 | X M D | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype:wildtype sibling|agent:n1 | GSM1289478 | GSM1289478: X M D ; Danio rerio; RNA Seq | GSM1289478 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1289478 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP034513 | X-M-D-.csfasta.gz X-M-D-.qual | SOLiD_native SOLiD_native | 522827305.0 | 14937923.0 | GSM1289478 r1 | 0:35 | 0:143962506;1:130748449;2:106995057;3:140038917;.:1082376 | 35 | SRX392658 | SRS515656 | SRA117588 | GEO | National University of Singapore | 1 | 0.02926 | 0.00817 | 0.99022 | 0.53421 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-16 | Adult | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37277 | 37277 | SRR1057959 | SRX398517 | SRS518969 | SRP034710 | PRJNA232516 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE53630 | Transcriptome Analysis | The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system | pubmed:24633177 | 6T2 | GSM1297515 | source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis | 6T2 | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor | one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis | GSM1297515 | GSM1297515: 6T2; Danio rerio; RNA Seq | GSM1297515 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1297515 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP034710 | 6T2.csfasta.gz 6T2.qual.gz | SOLiD_native SOLiD_native | 818910190.0 | 23397434.0 | GSM1297515 r1 | 0:35 | 0:347259734;1:164743259;2:162029194;3:130508344;.:14369659 | 35 | SRX398517 | SRS518969 | SRA122333 | GEO | National University of Singapore | 1 | 0.03756 | 0.0064 | 0.99931 | 0.92063 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-24 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37278 | 37278 | SRR1057958 | SRX398516 | SRS518968 | SRP034710 | PRJNA232516 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE53630 | Transcriptome Analysis | The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system | pubmed:24633177 | 6T1 | GSM1297514 | source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis | 6T1 | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | liver tumor | one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis | GSM1297514 | GSM1297514: 6T1; Danio rerio; RNA Seq | GSM1297514 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1297514 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP034710 | 6T1.csfasta.gz 6T1.qual.gz | SOLiD_native SOLiD_native | 761241005.0 | 21749743.0 | GSM1297514 r1 | 0:35 | 0:306840116;1:164725874;2:160786359;3:126370697;.:2517959 | 35 | SRX398516 | SRS518968 | SRA122333 | GEO | National University of Singapore | 1 | 0.0542 | 0.00664 | 0.99876 | 0.95184 | 35 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-24 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37279 | 37279 | SRR1057957 | SRX398515 | SRS518967 | SRP034710 | PRJNA232516 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE53630 | Transcriptome Analysis | The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system | pubmed:24633177 | 6M2 | GSM1297513 | source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control | 6M2 | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control | GSM1297513 | GSM1297513: 6M2; Danio rerio; RNA Seq | GSM1297513 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1297513 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP034710 | 6M2.csfasta.gz 6M2.qual.gz | SOLiD_native SOLiD_native | 627546330.0 | 20918211.0 | GSM1297513 r1 | 0:30 | 0:265606277;1:113800100;2:158432886;3:89099865;.:607202 | 30 | SRX398515 | SRS518967 | SRA122333 | GEO | National University of Singapore | 1 | 0.28369 | 0.05854 | 0.97611 | 0.92541 | 30 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-24 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37280 | 37280 | SRR1057956 | SRX398514 | SRS518966 | SRP034710 | PRJNA232516 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE53630 | Transcriptome Analysis | The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system | pubmed:24633177 | 6M1 | GSM1297512 | source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control | 6M1 | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. | control liver | one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control | GSM1297512 | GSM1297512: 6M1; Danio rerio; RNA Seq | GSM1297512 | 1 | Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. | GEO Accession:GSM1297512 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD 3 Plus System | SRP034710 | 6M1.csfasta.gz 6M1.qual.gz | SOLiD_native SOLiD_native | 670343910.0 | 22344797.0 | GSM1297512 r1 | 0:30 | 0:270812672;1:123662771;2:177982653;3:97335698;.:550116 | 30 | SRX398514 | SRS518966 | SRA122333 | GEO | National University of Singapore | 1 | 0.28477 | 0.05061 | 0.9735 | 0.86701 | 30 | B | usable mapping rate | legacy | early | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2013-12-24 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 37907 | 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 | 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 | |||||||||||||||||||||
| 41811 | 41811 | SRR5196075 | SRX2511746 | SRS1935439 | SRP097636 | PRJNA362941 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE93965 | Transcriptome Analysis | The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing. | pubmed:31827597 | CarcinomaM | GSM2465779 | source name:Hepatocellular carcinoma of transgenic fishes post mifeprist1 withdrawal|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | CarcinomaM | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample | Hepatocellular carcinoma of transgenic fishes post mifepristone withdrawal | One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | GSM2465779 | GSM2465779: CarcinomaM; Danio rerio; RNA Seq | GSM2465779 | 1 | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | GEO Accession:GSM2465779 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP097636 | solid_SAGE_6T2_F3.csfasta.gz solid_SAGE_6T2_F3_QV.qual.gz | SOLiD_native SOLiD_native | 818910190.0 | 23397434.0 | GSM2465779 r1 | 0:35 | 0:347259734;1:164743259;2:162029194;3:130508344;.:14369659 | 35 | SRX2511746 | SRS1935439 | SRA530985 | GEO | The Biomedical Center | 1 | 0.03756 | 0.00615 | 0.99928 | 0.91338 | 35 | B | usable mapping rate | legacy | early | unknown | poly_a | unknown | bulk | unknown | unknown | Unknown | 2017-01-23 | Undetermined | Adult | Cancer or Tumor | Cancer or Tumor | |||||||||||||||||||||||
| 41812 | 41812 | SRR5196074 | SRX2511745 | SRS1935438 | SRP097636 | PRJNA362941 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE93965 | Transcriptome Analysis | The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing. | pubmed:31827597 | Carcinoma | GSM2465778 | source name:Hepatocellular carcinoma of transgenic fishes|tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | Carcinoma | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample | Hepatocellular carcinoma of transgenic fishes | One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | tissue:Hepatocellular carcinoma|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | GSM2465778 | GSM2465778: Carcinoma; Danio rerio; RNA Seq | GSM2465778 | 1 | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | GEO Accession:GSM2465778 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP097636 | solid_SAGE_6T1_F3.csfasta.gz solid_SAGE_6T1_F3_QV.qual.gz | SOLiD_native SOLiD_native | 761241005.0 | 21749743.0 | GSM2465778 r1 | 0:35 | 0:306840116;1:164725874;2:160786359;3:126370697;.:2517959 | 35 | SRX2511745 | SRS1935438 | SRA530985 | GEO | The Biomedical Center | 1 | 0.0543 | 0.00668 | 0.9988 | 0.95092 | 35 | B | usable mapping rate | legacy | early | unknown | poly_a | unknown | bulk | unknown | unknown | Unknown | 2017-01-23 | Undetermined | Adult | Cancer or Tumor | Cancer or Tumor | |||||||||||||||||||||||
| 41813 | 41813 | SRR5196073 | SRX2511744 | SRS1935437 | SRP097636 | PRJNA362941 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE93965 | Transcriptome Analysis | The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing. | pubmed:31827597 | NormM | GSM2465777 | source name:Normal liver of transgenic fishes under mifeprist1|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | NormM | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample | Normal liver of transgenic fishes under mifepristone | One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | GSM2465777 | GSM2465777: NormM; Danio rerio; RNA Seq | GSM2465777 | 1 | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | GEO Accession:GSM2465777 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP097636 | solid_SAGE3_6M2_F3.csfasta.gz solid_SAGE3_6M2_F3_QV.qual.gz | SOLiD_native SOLiD_native | 627546330.0 | 20918211.0 | GSM2465777 r1 | 0:30 | 0:265606277;1:113800100;2:158432886;3:89099865;.:607202 | 30 | SRX2511744 | SRS1935437 | SRA530985 | GEO | The Biomedical Center | 1 | 0.28369 | 0.05854 | 0.97605 | 0.92502 | 30 | B | usable mapping rate | legacy | early | unknown | poly_a | unknown | bulk | unknown | unknown | Unknown | 2017-01-23 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 41814 | 41814 | SRR5196072 | SRX2511743 | SRS1935436 | SRP097636 | PRJNA362941 | Transcriptomic analyses of Kras induced zebrafish liver cancer | GSE93965 | Transcriptome Analysis | The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing. | pubmed:31827597 | Norm | GSM2465776 | source name:Normal liver of transgenic fishes|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | Norm | The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample | Normal liver of transgenic fishes | One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line | GSM2465776 | GSM2465776: Norm; Danio rerio; RNA Seq | GSM2465776 | 1 | mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample | GEO Accession:GSM2465776 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | SRP097636 | solid_SAGE3_6M1_F3.csfasta.gz solid_SAGE3_6M1_F3_QV.qual.gz | SOLiD_native SOLiD_native | 670343910.0 | 22344797.0 | GSM2465776 r1 | 0:30 | 0:270812672;1:123662771;2:177982653;3:97335698;.:550116 | 30 | SRX2511743 | SRS1935436 | SRA530985 | GEO | The Biomedical Center | 1 | 0.28477 | 0.05056 | 0.97348 | 0.86678 | 30 | B | usable mapping rate | legacy | early | unknown | poly_a | unknown | bulk | unknown | unknown | Unknown | 2017-01-23 | Undetermined | Adult | Liver | Liver and Biliary System | |||||||||||||||||||||||
| 48021 | 48021 | SRR6915090 | SRX3862779 | SRS3104834 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 10dpa replicate3 | GSM3071386 | source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 10dpa replicate3 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 10 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071386 | GSM3071386: 10dpa replicate3; Danio rerio; RNA Seq | GSM3071386 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071386 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam | bam | 682375516.0 | 14088728.0 | GSM3071386 r1 | 0:48.43 | A:140419665;C:148759068;G:176799261;T:168695522;N:47702000 | 48 | 140419665 | 148759068 | 176799261 | 168695522 | 47702000 | SRX3862779 | SRS3104834 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.76603 | 0.04459 | 0.79752 | 0.50424 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48022 | 48022 | SRR6915089 | SRX3862778 | SRS3104833 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 3dpa replicate3 | GSM3071385 | source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 3dpa replicate3 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 3 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071385 | GSM3071385: 3dpa replicate3; Danio rerio; RNA Seq | GSM3071385 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071385 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam | bam | 901887293.0 | 18522789.0 | GSM3071385 r1 | 0:48.69 | A:184300673;C:193849264;G:243428119;T:224471972;N:55837265 | 48 | 184300673 | 193849264 | 243428119 | 224471972 | 55837265 | SRX3862778 | SRS3104833 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.78632 | 0.03154 | 0.79707 | 0.51779 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48023 | 48023 | SRR6915088 | SRX3862777 | SRS3104832 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 2dpa replicate3 | GSM3071384 | source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 2dpa replicate3 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 2 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071384 | GSM3071384: 2dpa replicate3; Danio rerio; RNA Seq | GSM3071384 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071384 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam | bam | 850810410.0 | 17462158.0 | GSM3071384 r1 | 0:48.72 | A:176186499;C:182052044;G:228063922;T:213571294;N:50936651 | 48 | 176186499 | 182052044 | 228063922 | 213571294 | 50936651 | SRX3862777 | SRS3104832 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.77804 | 0.03462 | 0.80229 | 0.49822 | 43 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48024 | 48024 | SRR6915087 | SRX3862776 | SRS3104831 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 0dpa replicate3 | GSM3071383 | source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 0dpa replicate3 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 0 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071383 | GSM3071383: 0dpa replicate3; Danio rerio; RNA Seq | GSM3071383 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071383 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam | bam | 598710241.0 | 12328728.0 | GSM3071383 r1 | 0:48.56 | A:121889198;C:129444719;G:158430979;T:150128070;N:38817275 | 48 | 121889198 | 129444719 | 158430979 | 150128070 | 38817275 | SRX3862776 | SRS3104831 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.77 | 0.03334 | 0.799 | 0.45925 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48025 | 48025 | SRR6915086 | SRX3862775 | SRS3104830 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 10dpa replicate2 | GSM3071382 | source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 10dpa replicate2 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 10 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071382 | GSM3071382: 10dpa replicate2; Danio rerio; RNA Seq | GSM3071382 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071382 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam | bam | 1205021238.0 | 24639106.0 | GSM3071382 r1 | 0:48.91 | A:255022070;C:275793907;G:309172527;T:294800027;N:70232707 | 48 | 255022070 | 275793907 | 309172527 | 294800027 | 70232707 | SRX3862775 | SRS3104830 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.80398 | 0.05829 | 0.78644 | 0.4993 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48026 | 48026 | SRR6915085 | SRX3862774 | SRS3104829 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 3dpa replicate2 | GSM3071381 | source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 3dpa replicate2 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 3 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071381 | GSM3071381: 3dpa replicate2; Danio rerio; RNA Seq | GSM3071381 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071381 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam | bam | 1479531813.0 | 30219937.0 | GSM3071381 r1 | 0:48.96 | A:314793261;C:331769330;G:384109921;T:369987947;N:78871354 | 48 | 314793261 | 331769330 | 384109921 | 369987947 | 78871354 | SRX3862774 | SRS3104829 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.81777 | 0.03195 | 0.7821 | 0.49263 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48027 | 48027 | SRR6915084 | SRX3862773 | SRS3104828 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 2dpa replicate2 | GSM3071380 | source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 2dpa replicate2 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 2 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071380 | GSM3071380: 2dpa replicate2; Danio rerio; RNA Seq | GSM3071380 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071380 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam | bam | 834856811.0 | 17079585.0 | GSM3071380 r1 | 0:48.88 | A:179851654;C:186667201;G:209784080;T:212166083;N:46387793 | 48 | 179851654 | 186667201 | 209784080 | 212166083 | 46387793 | SRX3862773 | SRS3104828 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.80341 | 0.02786 | 0.78031 | 0.49876 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48028 | 48028 | SRR6915083 | SRX3862772 | SRS3104827 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 0dpa replicate2 | GSM3071379 | source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 0dpa replicate2 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 0 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071379 | GSM3071379: 0dpa replicate2; Danio rerio; RNA Seq | GSM3071379 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071379 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam | bam | 821645371.0 | 16824250.0 | GSM3071379 r1 | 0:48.84 | A:169383232;C:176200663;G:223364159;T:207905438;N:44791879 | 48 | 169383232 | 176200663 | 223364159 | 207905438 | 44791879 | SRX3862772 | SRS3104827 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.79697 | 0.04152 | 0.79513 | 0.48078 | 34 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48029 | 48029 | SRR6915082 | SRX3862771 | SRS3104826 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 10dpa replicate1 | GSM3071378 | source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 10dpa replicate1 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 10 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071378 | GSM3071378: 10dpa replicate1; Danio rerio; RNA Seq | GSM3071378 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071378 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam | bam | 1056921416.0 | 21553661.0 | GSM3071378 r1 | 0:49.04 | A:223138065;C:233998717;G:286278215;T:261736901;N:51769518 | 49 | 223138065 | 233998717 | 286278215 | 261736901 | 51769518 | SRX3862771 | SRS3104826 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.81372 | 0.06015 | 0.79017 | 0.49818 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48030 | 48030 | SRR6915081 | SRX3862770 | SRS3104824 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 3dpa replicate1 | GSM3071377 | source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 3dpa replicate1 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 3 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071377 | GSM3071377: 3dpa replicate1; Danio rerio; RNA Seq | GSM3071377 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071377 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam | bam | 614372216.0 | 12531168.0 | GSM3071377 r1 | 0:49.03 | A:129828689;C:133826356;G:168985348;T:153858339;N:27873484 | 49 | 129828689 | 133826356 | 168985348 | 153858339 | 27873484 | SRX3862770 | SRS3104824 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.81659 | 0.02803 | 0.78987 | 0.49295 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48031 | 48031 | SRR6915080 | SRX3862769 | SRS3104825 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 2dpa replicate1 | GSM3071376 | source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 2dpa replicate1 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 2 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071376 | GSM3071376: 2dpa replicate1; Danio rerio; RNA Seq | GSM3071376 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071376 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam | bam | 1317408760.0 | 26870813.0 | GSM3071376 r1 | 0:49.03 | A:278980295;C:285236037;G:357022664;T:334390621;N:61779143 | 49 | 278980295 | 285236037 | 357022664 | 334390621 | 61779143 | SRX3862769 | SRS3104825 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.81546 | 0.02559 | 0.79328 | 0.48857 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure | ||||||||||||||||
| 48032 | 48032 | SRR6915079 | SRX3862768 | SRS3104823 | SRP136710 | PRJNA447984 | RNA seq data from adult zebrafish caudal fin regeneration | GSE112498 | Transcriptome Analysis | Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2 3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples. | pubmed:30031067 | 0dpa replicate1 | GSM3071375 | source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | 0dpa replicate1 | SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample | caudal fin tissue 0 dy post amputation | Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at 80°C before RNA extraction. | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples. | tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf | GSM3071375 | GSM3071375: 0dpa replicate1; Danio rerio; RNA Seq | GSM3071375 | 1 | RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer. | GEO Accession:GSM3071375 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB 5500 Genetic Analyzer | SRP136710 | options: accept hard clip | Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam | bam | 975324708.0 | 19881338.0 | GSM3071375 r1 | 0:49.06 | A:203549346;C:215407985;G:265949502;T:244027187;N:46390688 | 49 | 203549346 | 215407985 | 265949502 | 244027187 | 46390688 | SRX3862768 | SRS3104823 | SRA676352 | GEO | Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon | 1 | 0.80817 | 0.05047 | 0.79569 | 0.47149 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | lexogen | bulk | unknown | unknown | France | 2018-03-29 | Adult | Adult | Fin | Surface Structure |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;